push-uzomzootkrpy #5
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+2
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@@ -9,4 +9,5 @@
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/web_src/**/*_files
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/web_src/**/*_cache
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/.luarc.json
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*.log
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/sandbox
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*.log
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@@ -1,897 +0,0 @@
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{
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||||
"cells": [
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||||
{
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||||
"cell_type": "markdown",
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||||
"id": "30438c30",
|
||||
"metadata": {},
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||||
"source": [
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||||
"# Unix Essentials — Bash Practice Notebook\n",
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"\n",
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||||
"This notebook contains 50 small Bash exercises grouped by topic.\n",
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||||
"Each exercise includes a hidden solution that can be revealed in Jupyter."
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||||
]
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||||
},
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||||
{
|
||||
"cell_type": "markdown",
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||||
"id": "39d711f9",
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||||
"metadata": {},
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||||
"source": [
|
||||
"## Series 1 — Paths and Directories"
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]
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||||
},
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||||
{
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||||
"cell_type": "markdown",
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||||
"id": "6fb7335e",
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||||
"metadata": {},
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||||
"source": [
|
||||
"### Exercise 1.1 — Show your current working directory"
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||||
]
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||||
},
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||||
{
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||||
"cell_type": "code",
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||||
"execution_count": null,
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||||
"id": "2b8575f3",
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||||
"metadata": {},
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||||
"outputs": [],
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||||
"source": [
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||||
"# your work here\n",
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||||
"pwd"
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||||
]
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||||
},
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||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
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||||
"id": "21f63bb0",
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||||
"metadata": {
|
||||
"jupyter": {
|
||||
"outputs_hidden": true,
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||||
"source_hidden": true
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||||
}
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||||
},
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||||
"outputs": [],
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||||
"source": [
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||||
"# Solution\n",
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||||
"pwd"
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||||
]
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||||
},
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||||
{
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||||
"cell_type": "markdown",
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||||
"id": "61a624bf",
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||||
"metadata": {},
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||||
"source": [
|
||||
"### Exercise 1.2 — Create a new directory named `testdir`"
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||||
]
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||||
},
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||||
{
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||||
"cell_type": "code",
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||||
"execution_count": null,
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||||
"id": "4a4df387",
|
||||
"metadata": {},
|
||||
"outputs": [],
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||||
"source": [
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||||
"# your work here\n",
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"mkdir testdir"
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]
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||||
},
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||||
{
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||||
"cell_type": "code",
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||||
"execution_count": null,
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||||
"id": "2b5cfbca",
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||||
"metadata": {
|
||||
"jupyter": {
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||||
"outputs_hidden": true,
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||||
"source_hidden": true
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||||
}
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||||
},
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||||
"outputs": [],
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||||
"source": [
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||||
"# Solution\n",
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"mkdir testdir"
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]
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||||
},
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||||
{
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||||
"cell_type": "markdown",
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||||
"id": "2dccbb61",
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||||
"metadata": {},
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||||
"source": [
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||||
"### Exercise 1.3 — Move into `testdir` using a relative path"
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]
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},
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||||
{
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||||
"cell_type": "code",
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||||
"execution_count": null,
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||||
"id": "fb73ca3c",
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||||
"metadata": {},
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||||
"outputs": [],
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||||
"source": [
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"# your work here\n",
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"cd testdir"
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]
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},
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{
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||||
"cell_type": "code",
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"execution_count": null,
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"id": "ba670a20",
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||||
"metadata": {
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||||
"jupyter": {
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||||
"outputs_hidden": true,
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||||
"source_hidden": true
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}
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||||
},
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||||
"outputs": [],
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"source": [
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"# Solution\n",
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"cd testdir"
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]
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},
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{
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"cell_type": "markdown",
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"id": "4f7e5817",
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"metadata": {},
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||||
"source": [
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||||
"### Exercise 1.4 — Create two subdirectories `a` and `b` in one command"
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]
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},
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||||
{
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||||
"cell_type": "code",
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||||
"execution_count": null,
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"id": "30be8f44",
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||||
"metadata": {},
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||||
"outputs": [],
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||||
"source": [
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"# your work here\n",
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"mkdir a b"
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]
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},
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{
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||||
"cell_type": "code",
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||||
"execution_count": null,
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"id": "caf92714",
|
||||
"metadata": {
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||||
"jupyter": {
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||||
"outputs_hidden": true,
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"source_hidden": true
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}
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},
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||||
"outputs": [],
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||||
"source": [
|
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"# Solution\n",
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"mkdir a b"
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]
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},
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||||
{
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||||
"cell_type": "markdown",
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"id": "edec9041",
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"metadata": {},
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"source": [
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"### Exercise 1.5 — Return to the parent directory using `..`"
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]
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||||
},
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||||
{
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||||
"cell_type": "code",
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"execution_count": null,
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"id": "32a0f1df",
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||||
"metadata": {},
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||||
"outputs": [],
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||||
"source": [
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||||
"# your work here\n",
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"cd .."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "2a0aa92f",
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"metadata": {
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||||
"jupyter": {
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||||
"outputs_hidden": true,
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"source_hidden": true
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}
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},
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"outputs": [],
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"source": [
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"# Solution\n",
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||||
"cd .."
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]
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||||
},
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{
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||||
"cell_type": "markdown",
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"id": "31917159",
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||||
"metadata": {},
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||||
"source": [
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||||
"### Exercise 1.6 — Create nested directories `one/two/three` in a single command"
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]
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||||
},
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||||
{
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||||
"cell_type": "code",
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"execution_count": null,
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"id": "c0a313c3",
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||||
"metadata": {},
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||||
"outputs": [],
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||||
"source": [
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"# your work here\n",
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"mkdir -p one/two/three"
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]
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},
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{
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||||
"cell_type": "code",
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"execution_count": null,
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"id": "4af63dce",
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||||
"metadata": {
|
||||
"jupyter": {
|
||||
"outputs_hidden": true,
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||||
"source_hidden": true
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||||
}
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||||
},
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||||
"outputs": [],
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||||
"source": [
|
||||
"# Solution\n",
|
||||
"mkdir -p one/two/three"
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||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
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||||
"id": "24ee949e",
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||||
"metadata": {},
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||||
"source": [
|
||||
"### Exercise 1.7 — List the absolute path of the current directory"
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]
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||||
},
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||||
{
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||||
"cell_type": "code",
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||||
"execution_count": null,
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||||
"id": "8258fff7",
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||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# your work here\n",
|
||||
"pwd"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
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||||
"execution_count": null,
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||||
"id": "a6a062b2",
|
||||
"metadata": {
|
||||
"jupyter": {
|
||||
"outputs_hidden": true,
|
||||
"source_hidden": true
|
||||
}
|
||||
},
|
||||
"outputs": [],
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||||
"source": [
|
||||
"# Solution\n",
|
||||
"pwd"
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||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
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||||
"id": "6d724d3e",
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||||
"metadata": {},
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||||
"source": [
|
||||
"### Exercise 1.8 — Create a directory using an absolute path"
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||||
]
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||||
},
|
||||
{
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||||
"cell_type": "code",
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||||
"execution_count": null,
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||||
"id": "5f497f7c",
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||||
"metadata": {},
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||||
"outputs": [],
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||||
"source": [
|
||||
"# your work here\n",
|
||||
"mkdir /tmp/mydir"
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||||
]
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||||
},
|
||||
{
|
||||
"cell_type": "code",
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||||
"execution_count": null,
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||||
"id": "1d1d4e27",
|
||||
"metadata": {
|
||||
"jupyter": {
|
||||
"outputs_hidden": true,
|
||||
"source_hidden": true
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||||
}
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||||
},
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||||
"outputs": [],
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||||
"source": [
|
||||
"# Solution\n",
|
||||
"mkdir /tmp/mydir"
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||||
]
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||||
},
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||||
{
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||||
"cell_type": "markdown",
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||||
"id": "0a4cbe5b",
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||||
"metadata": {},
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||||
"source": [
|
||||
"### Exercise 1.9 — Display both `.` and `..` directories with `ls -a`"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
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||||
"execution_count": null,
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||||
"id": "7d962a9f",
|
||||
"metadata": {},
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||||
"outputs": [],
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||||
"source": [
|
||||
"# your work here\n",
|
||||
"ls -a"
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||||
]
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||||
},
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||||
{
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||||
"cell_type": "code",
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||||
"execution_count": null,
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||||
"id": "91994de2",
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||||
"metadata": {
|
||||
"jupyter": {
|
||||
"outputs_hidden": true,
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||||
"source_hidden": true
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# Solution\n",
|
||||
"ls -a"
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||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"id": "e147ff34",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"### Exercise 1.10 — Remove the directory `/tmp/mydir`"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
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||||
"id": "dcae28e3",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# your work here\n",
|
||||
"rmdir /tmp/mydir"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
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||||
"id": "1a000f14",
|
||||
"metadata": {
|
||||
"jupyter": {
|
||||
"outputs_hidden": true,
|
||||
"source_hidden": true
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# Solution\n",
|
||||
"rmdir /tmp/mydir"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"id": "578548f7",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"## Series 2 — File Manipulation"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"id": "813140d5",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"### Exercise 2.1 — Create an empty file named `notes.txt`"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "08385872",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"touch notes.txt"
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||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "a474ad37",
|
||||
"metadata": {
|
||||
"jupyter": {
|
||||
"outputs_hidden": true,
|
||||
"source_hidden": true
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# Solution\n",
|
||||
"touch notes.txt"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"id": "6e918f3d",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"### Exercise 2.2 — Copy `notes.txt` to `backup.txt`"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "faf85985",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"cp notes.txt backup.txt"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "4d3e54d5",
|
||||
"metadata": {
|
||||
"jupyter": {
|
||||
"outputs_hidden": true,
|
||||
"source_hidden": true
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# Solution\n",
|
||||
"cp notes.txt backup.txt"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"id": "2c924f2e",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"### Exercise 2.3 — Rename `backup.txt` to `archive.txt`"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "2d4adeb4",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"mv backup.txt archive.txt"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "2c62e70f",
|
||||
"metadata": {
|
||||
"jupyter": {
|
||||
"outputs_hidden": true,
|
||||
"source_hidden": true
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# Solution\n",
|
||||
"mv backup.txt archive.txt"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"id": "c9e525a7",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"### Exercise 2.4 — Create 3 files and remove one with `rm`"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "3ef53a3a",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"touch a.txt b.txt c.txt\n",
|
||||
"rm b.txt"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "55e07074",
|
||||
"metadata": {
|
||||
"jupyter": {
|
||||
"outputs_hidden": true,
|
||||
"source_hidden": true
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# Solution\n",
|
||||
"touch a.txt b.txt c.txt\n",
|
||||
"rm b.txt"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"id": "b5a406b4",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"### Exercise 2.5 — Remove a directory recursively"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "2c819a49",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"mkdir -p tmpdir/sub\n",
|
||||
"rm -rf tmpdir"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "b958a668",
|
||||
"metadata": {
|
||||
"jupyter": {
|
||||
"outputs_hidden": true,
|
||||
"source_hidden": true
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# Solution\n",
|
||||
"mkdir -p tmpdir/sub\n",
|
||||
"rm -rf tmpdir"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"id": "9aa4996e",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"## Series 3 — Redirections and Pipes"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"id": "ada90797",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"### Exercise 3.1 — Save the output of `ls` to a file `list.txt`"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "25afa75b",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"ls > list.txt"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "80ca4767",
|
||||
"metadata": {
|
||||
"jupyter": {
|
||||
"outputs_hidden": true,
|
||||
"source_hidden": true
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# Solution\n",
|
||||
"ls > list.txt"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"id": "61c3bff6",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"### Exercise 3.2 — Append the date to `list.txt`"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "b7849f15",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"date >> list.txt"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "83b08fe6",
|
||||
"metadata": {
|
||||
"jupyter": {
|
||||
"outputs_hidden": true,
|
||||
"source_hidden": true
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# Solution\n",
|
||||
"date >> list.txt"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"id": "600edcaa",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"### Exercise 3.3 — Count lines of `list.txt` with a pipe"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "37e859f4",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"cat list.txt | wc -l"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "d1429a1c",
|
||||
"metadata": {
|
||||
"jupyter": {
|
||||
"outputs_hidden": true,
|
||||
"source_hidden": true
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# Solution\n",
|
||||
"cat list.txt | wc -l"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"id": "a901cf34",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"### Exercise 3.4 — Redirect error messages to a file"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "f2c1d530",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"ls /fakepath 2> errors.txt"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "66c68bc4",
|
||||
"metadata": {
|
||||
"jupyter": {
|
||||
"outputs_hidden": true,
|
||||
"source_hidden": true
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# Solution\n",
|
||||
"ls /fakepath 2> errors.txt"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"id": "72e5eca4",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"## Series 4 — Viewing Results"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"id": "dd7cbf2e",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"### Exercise 4.1 — Display the first 5 lines of `/etc/passwd`"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "195c0f25",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"head -5 /etc/passwd"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "72dc0297",
|
||||
"metadata": {
|
||||
"jupyter": {
|
||||
"outputs_hidden": true,
|
||||
"source_hidden": true
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# Solution\n",
|
||||
"head -5 /etc/passwd"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"id": "227ebdf8",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"### Exercise 4.2 — Show the last 3 lines of `/etc/passwd`"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "3a829074",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"tail -3 /etc/passwd"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "e66f1752",
|
||||
"metadata": {
|
||||
"jupyter": {
|
||||
"outputs_hidden": true,
|
||||
"source_hidden": true
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# Solution\n",
|
||||
"tail -3 /etc/passwd"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"id": "826cbb41",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"### Exercise 4.3 — Use `grep` to show lines containing 'root'"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "df9a877b",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"grep root /etc/passwd"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "5ed43d3d",
|
||||
"metadata": {
|
||||
"jupyter": {
|
||||
"outputs_hidden": true,
|
||||
"source_hidden": true
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# Solution\n",
|
||||
"grep root /etc/passwd"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"id": "a6c2f0a8",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"## Series 5 — Process Management"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"id": "333ab7c1",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"### Exercise 5.1 — List current processes"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "41dc9dfb",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"ps"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "c0f28455",
|
||||
"metadata": {
|
||||
"jupyter": {
|
||||
"outputs_hidden": true,
|
||||
"source_hidden": true
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# Solution\n",
|
||||
"ps"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"id": "c2d37e8f",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"### Exercise 5.2 — Display dynamic process list with `top`"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "7931c9aa",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"top"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "947570cf",
|
||||
"metadata": {
|
||||
"jupyter": {
|
||||
"outputs_hidden": true,
|
||||
"source_hidden": true
|
||||
}
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"# Solution\n",
|
||||
"top"
|
||||
]
|
||||
}
|
||||
],
|
||||
"metadata": {
|
||||
"kernelspec": {
|
||||
"display_name": "Bash",
|
||||
"language": "bash",
|
||||
"name": "bash"
|
||||
},
|
||||
"language_info": {
|
||||
"name": "bash"
|
||||
}
|
||||
},
|
||||
"nbformat": 4,
|
||||
"nbformat_minor": 5
|
||||
}
|
||||
File diff suppressed because it is too large.
Load diff
@@ -115,6 +115,7 @@
|
||||
<nav>
|
||||
<ul id="nav-menu"></ul>
|
||||
<ul class="admin-links">
|
||||
<li><a href="/obidoc/" target="_blank">OBITools 4 Doc</a></li>
|
||||
<li><a href="/jupyter/" target="_blank">JupyterHub</a></li>
|
||||
<li><a href="/sftp/" target="_blank">Data Admin</a></li>
|
||||
</ul>
|
||||
|
||||
@@ -0,0 +1,56 @@
|
||||
<!DOCTYPE html>
|
||||
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|
||||
|
||||
<head>
|
||||
<meta charset="UTF-8">
|
||||
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|
||||
<meta name="description" content="">
|
||||
<meta name="theme-color" media="(prefers-color-scheme: light)" content="#ffffff">
|
||||
<meta name="theme-color" media="(prefers-color-scheme: dark)" content="#343a40">
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||||
<meta name="color-scheme" content="light dark"><meta property="og:url" content="http://metabar:8888/obidoc/404.html">
|
||||
<meta property="og:site_name" content="OBITools4 documentation">
|
||||
<meta property="og:title" content="404 Page not found">
|
||||
<meta property="og:locale" content="en_us">
|
||||
<meta property="og:type" content="website">
|
||||
<title>404 Page not found | OBITools4 documentation</title>
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||||
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||||
<link rel="manifest" href="/obidoc/manifest.json">
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<script defer src="/obidoc/fuse.min.js"></script>
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<script defer src="/obidoc/en.search.min.4da51bdd2d833922fdbc0e19df517221387fc625ffb68ee140d605b3c5b68058.js" integrity="sha256-TaUb3S2DOSL9vA4Z31FyITh/xiX/to7hQNYFs8W2gFg=" crossorigin="anonymous"></script>
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<script defer src="/obidoc/sw.min.32af8eafce4180aa1c5dea66d99fb26ba9043ea7c7a4c706138c91d9051b285e.js" integrity="sha256-Mq+Or85BgKocXepm2Z+ya6kEPqfHpMcGE4yR2QUbKF4=" crossorigin="anonymous"></script>
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|
||||
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||||
https://github.com/alex-shpak/hugo-book
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<link rel="stylesheet" type="text/css" href="http://metabar:8888/obidoc/hugo-cite.css" />
|
||||
|
||||
<style>
|
||||
.not-found {
|
||||
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|
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||||
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|
||||
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|
||||
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|
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|
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|
||||
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|
||||
</head>
|
||||
|
||||
<body>
|
||||
<main class="flex justify-center not-found">
|
||||
<div>
|
||||
<h1>404</h1>
|
||||
<h2>Page Not Found</h2>
|
||||
<h3>
|
||||
<a href="/obidoc/">OBITools4 documentation</a>
|
||||
</h3>
|
||||
</div>
|
||||
</main>
|
||||
|
||||
|
||||
</body>
|
||||
|
||||
</html>
|
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+1
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<title>Categories on OBITools4 documentation</title>
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<link>http://metabar:8888/obidoc/categories/</link>
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truncated
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truncated
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"type": "mesh3d",
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"frame": null
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}
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],
|
||||
"highlight": {
|
||||
"on": "plotly_click",
|
||||
"persistent": false,
|
||||
"dynamic": false,
|
||||
"selectize": false,
|
||||
"opacityDim": 0.20000000000000001,
|
||||
"selected": {
|
||||
"opacity": 1
|
||||
},
|
||||
"debounce": 0
|
||||
},
|
||||
"shinyEvents": ["plotly_hover", "plotly_click", "plotly_selected", "plotly_relayout", "plotly_brushed", "plotly_brushing", "plotly_clickannotation", "plotly_doubleclick", "plotly_deselect", "plotly_afterplot", "plotly_sunburstclick"],
|
||||
"base_url": "https://plot.ly"
|
||||
}
|
||||
+149
@@ -0,0 +1,149 @@
|
||||
---
|
||||
title: "Untitled"
|
||||
format: html
|
||||
editor: visual
|
||||
---
|
||||
|
||||
```{r}
|
||||
library(tidyverse)
|
||||
library(plotly)
|
||||
library(matrixStats)
|
||||
```
|
||||
|
||||
```{r}
|
||||
log_sum_exp <- function(a,b) {
|
||||
m <- map2_dbl(a,b,max)
|
||||
m + log(exp(a-m)+exp(b-m))
|
||||
}
|
||||
```
|
||||
|
||||
$$
|
||||
\log(1 - e^b) = \log\left(-e^{(1-b)}\right)
|
||||
$$
|
||||
|
||||
```{r}
|
||||
log1m_exp <- function(b) {
|
||||
if (any(b >= 0)) {
|
||||
stop(glue::glue("b must be negative (b={b})"))
|
||||
}
|
||||
return(log(-expm1(b))) # expm1(b) = exp(b) - 1, pour éviter les erreurs d'arrondi
|
||||
}
|
||||
```
|
||||
|
||||
$$
|
||||
\log(e^a - e^b) = a + \log(1 - e^{b-a})
|
||||
$$
|
||||
|
||||
```{r}
|
||||
log_diff_exp <- function(a, b) {
|
||||
# Vérifier si a > b pour éviter des résultats indéfinis
|
||||
if (any(a < b)) {
|
||||
stop(glue::glue("Erreur : a ({a}) doit etre strictement sup�rieur � b ({b}) pour que e^a - e^b soit positif."))
|
||||
}
|
||||
|
||||
# Calculer log(e^a - e^b) de manière stable
|
||||
ifelse(a == b, -Inf,a + log1m_exp(b-a))
|
||||
}
|
||||
```
|
||||
|
||||
$$
|
||||
P_{error} = 10^{-\frac{Q}{10}}
|
||||
$$
|
||||
|
||||
$$
|
||||
\begin{aligned}
|
||||
q_F &= -\frac{Q_F}{10} \cdot \log(10) \\
|
||||
q_R &= -\frac{Q_R}{10} \cdot \log(10) \\
|
||||
P(macth | Obs(match)) &= (1-e^{q_F}) (1-e^{q_R}) + (1-e^{q_F})\frac{e^{q_R}}{4}+ (1-e^{q_R})\frac{e^{q_F}}{4} + \frac{e^{q_F+q_R}}{4} \\
|
||||
&=1 - e^{q_R} - e^{q_F} + e^{q_F+q_R} + \frac{e^{q_R}}{4} - \frac{e^{q_F+q_R}}{4} + \frac{e^{q_F}}{4} - \frac{e^{q_F+q_R}}{4} + \frac{e^{q_F+q_R}}{4} \\
|
||||
&= \frac{4 - 4e^{q_F} - 4e^{q_R} + 4e^{q_F+q_R} + e^{q_F} + e^{q_R} - e^{q_F+q_R}}{4} \\
|
||||
&= \frac{4 - 3e^{q_F}- 3e^{q_R} + 3e^{q_F+q_R}}{4}\\
|
||||
&= \frac{4 - 3(e^{q_F}+e^{q_R}-e^{q_F+q_R})}{4} \\
|
||||
&= 1 - \frac{3}{4}\left(e^{q_F}+e^{q_R}-e^{q_F+q_R}\right)
|
||||
\end{aligned}
|
||||
$$
|
||||
|
||||
```{r}
|
||||
Pm_match_observed <- function(Q_F, Q_R) {
|
||||
l10 <- log(10)
|
||||
l3 <- log(3)
|
||||
l4 <- log(4)
|
||||
|
||||
q_F <- -Q_F/10*l10
|
||||
q_R <- -Q_R/10*l10
|
||||
|
||||
term1 <- log_sum_exp(q_F,q_R)
|
||||
term2 <- log_diff_exp(term1,q_F+q_R) + l3 - l4
|
||||
|
||||
log1m_exp(term2)
|
||||
}
|
||||
```
|
||||
|
||||
$$
|
||||
\begin{aligned}
|
||||
P(macth | Obs(mismatch)) &= \frac{(1-e^{q_F})e^{q_R}}{4} + \frac{(1-e^{q_R})e^{q_F}}{4} + \frac{e^{q_F+q_R}}{4} \\
|
||||
&= \frac{(1-e^{q_F})e^{q_R} + (1-e^{q_R})e^{q_F} + e^{q_F+q_R}}{4} \\
|
||||
&= \frac{e^{q_R} - e^{q_F+q_R} + e^{q_F} - e^{q_F+q_R} + e^{q_F+q_R}}{4} \\
|
||||
&= \frac{e^{q_F} + e^{q_R} - e^{q_F+q_R}}{4}
|
||||
\end{aligned}
|
||||
$$
|
||||
|
||||
```{r}
|
||||
Pm_mismatch_observed <- function(Q_F, Q_R) {
|
||||
l10 <- log(10)
|
||||
l3 <- log(3)
|
||||
l4 <- log(4)
|
||||
|
||||
q_F <- -Q_F/10*l10
|
||||
q_R <- -Q_R/10*l10
|
||||
|
||||
term1 <- log_sum_exp(q_F,q_R)
|
||||
log_diff_exp(term1,q_F+q_R) - l4
|
||||
}
|
||||
```
|
||||
|
||||
```{r}
|
||||
score_match_observed <- function(Q_F, Q_R) {
|
||||
Pm_match_observed(Q_F,Q_R) - log1m_exp(Pm_match_observed(Q_F,Q_R))
|
||||
}
|
||||
|
||||
score_mismatch_observed <- function(Q_F, Q_R) {
|
||||
Pm_mismatch_observed(Q_F,Q_R) - log1m_exp(Pm_mismatch_observed(Q_F,Q_R))
|
||||
}
|
||||
```
|
||||
|
||||
```{r}
|
||||
scores <- expand_grid(QF=0:40,QR=0:40) %>%
|
||||
mutate(score_match_observed = round(score_match_observed(QF,QR),2),
|
||||
score_mismatch_observed = round(score_mismatch_observed(QF,QR),2))
|
||||
```
|
||||
|
||||
```{r}
|
||||
plot_match <- plot_ly(scores,
|
||||
x=~QF, y=~QR, z=~score_match_observed,
|
||||
type="mesh3d") %>%
|
||||
layout(
|
||||
plot_bgcolor = "#bababa",
|
||||
scene = list(
|
||||
xaxis = list(title = "Q forward read"), # Change x/y/z axis title
|
||||
yaxis = list(title = "Q reverse read"),
|
||||
zaxis = list(title = "Score match")))
|
||||
```
|
||||
|
||||
```{r}
|
||||
plot_mismatch <- plot_ly(scores,
|
||||
x=~QF, y=~QR, z=~score_mismatch_observed,
|
||||
type="mesh3d") %>%
|
||||
layout(
|
||||
plot_bgcolor = "#bababa",
|
||||
scene = list(
|
||||
xaxis = list(title = "Q forward read"), # Change x/y/z axis title
|
||||
yaxis = list(title = "Q reverse read"),
|
||||
zaxis = list(title = "Score mismatch")))
|
||||
```
|
||||
|
||||
```{r}
|
||||
write(plotly_json(plot_match,FALSE),"content/docs/commands/alignments/obipairing/exact-alignment/match.json")
|
||||
write(plotly_json(plot_mismatch,FALSE),"content/docs/commands/alignments/obipairing/exact-alignment/mismatch.json")
|
||||
|
||||
```
|
||||
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|
||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||
<channel>
|
||||
<title>The FASTA-like alignment on OBITools4 documentation</title>
|
||||
<link>http://metabar:8888/obidoc/docs/commands/alignments/obipairing/fasta-like/</link>
|
||||
<description>Recent content in The FASTA-like alignment on OBITools4 documentation</description>
|
||||
<generator>Hugo</generator>
|
||||
<language>en-us</language>
|
||||
<atom:link href="http://metabar:8888/obidoc/docs/commands/alignments/obipairing/fasta-like/index.xml" rel="self" type="application/rss+xml" />
|
||||
</channel>
|
||||
</rss>
|
||||
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|
||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||
<channel>
|
||||
<title>Basics on OBITools4 documentation</title>
|
||||
<link>http://metabar:8888/obidoc/docs/commands/basics/</link>
|
||||
<description>Recent content in Basics on OBITools4 documentation</description>
|
||||
<generator>Hugo</generator>
|
||||
<language>en-us</language>
|
||||
<lastBuildDate></lastBuildDate>
|
||||
<atom:link href="http://metabar:8888/obidoc/docs/commands/basics/index.xml" rel="self" type="application/rss+xml" />
|
||||
</channel>
|
||||
</rss>
|
||||
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|
||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||
<channel>
|
||||
<title>Demultiplexing samples on OBITools4 documentation</title>
|
||||
<link>http://metabar:8888/obidoc/docs/commands/demultiplexing/</link>
|
||||
<description>Recent content in Demultiplexing samples on OBITools4 documentation</description>
|
||||
<generator>Hugo</generator>
|
||||
<language>en-us</language>
|
||||
<lastBuildDate></lastBuildDate>
|
||||
<atom:link href="http://metabar:8888/obidoc/docs/commands/demultiplexing/index.xml" rel="self" type="application/rss+xml" />
|
||||
</channel>
|
||||
</rss>
|
||||
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|
||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||
<channel>
|
||||
<title>Experimentals on OBITools4 documentation</title>
|
||||
<link>http://metabar:8888/obidoc/docs/commands/experimental/</link>
|
||||
<description>Recent content in Experimentals on OBITools4 documentation</description>
|
||||
<generator>Hugo</generator>
|
||||
<language>en-us</language>
|
||||
<lastBuildDate></lastBuildDate>
|
||||
<atom:link href="http://metabar:8888/obidoc/docs/commands/experimental/index.xml" rel="self" type="application/rss+xml" />
|
||||
</channel>
|
||||
</rss>
|
||||
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|
||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||
<channel>
|
||||
<title>The OBITools4 commands on OBITools4 documentation</title>
|
||||
<link>http://metabar:8888/obidoc/docs/commands/</link>
|
||||
<description>Recent content in The OBITools4 commands on OBITools4 documentation</description>
|
||||
<generator>Hugo</generator>
|
||||
<language>en-us</language>
|
||||
<lastBuildDate>Fri, 04 Oct 2024 17:16:03 +0200</lastBuildDate>
|
||||
<atom:link href="http://metabar:8888/obidoc/docs/commands/index.xml" rel="self" type="application/rss+xml" />
|
||||
<item>
|
||||
<title>Glossary of tags</title>
|
||||
<link>http://metabar:8888/obidoc/docs/commands/tags/</link>
|
||||
<pubDate>Fri, 04 Oct 2024 17:16:03 +0200</pubDate>
|
||||
<guid>http://metabar:8888/obidoc/docs/commands/tags/</guid>
|
||||
<description><h1 id="glossary-of-tags">
 Glossary of tags
 <a class="anchor" href="#glossary-of-tags">#</a>
</h1>
<h3 id="--d--">
 - D -
 <a class="anchor" href="#--d--">#</a>
</h3>
<ul>
<li>
<p><strong>definition</strong> :</p>
<blockquote>
<p>text information about the sequence present in the original sequence file.</p>
</blockquote>
</li>
<li>
<p><strong>direction</strong> :</p>
<blockquote>
<p>set to “forward” if the original sequence did not need to be reverse-complemented to be processed, set to “reverse” otherwise.
(
 <a href="http://metabar:8888/obidoc/obitools/obipcr/">obipcr</a>)</p>
</blockquote>
</li>
</ul>
<h3 id="--f--">
 - F -
 <a class="anchor" href="#--f--">#</a>
</h3>
<ul>
<li>
<p><strong>forward_error</strong> :</p>
<blockquote>
<p>Number of mismatch between forward primer and priming site
(
 <a href="http://metabar:8888/obidoc/obitools/obipcr/">obipcr</a>)</p>
</blockquote>
</li>
<li>
<p><strong>forward_match</strong> :</p>
<blockquote>
<p>Forward primer priming site sequence
(
 <a href="http://metabar:8888/obidoc/obitools/obipcr/">obipcr</a>)</p>
</blockquote>
</li>
<li>
<p><strong>forward_primer</strong> :</p>
<blockquote>
<p>Forward primer sequence
(
 <a href="http://metabar:8888/obidoc/obitools/obipcr/">obipcr</a>)</p></description>
|
||||
</item>
|
||||
</channel>
|
||||
</rss>
|
||||
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@@ -0,0 +1,12 @@
|
||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||
<channel>
|
||||
<title>Shared command options on OBITools4 documentation</title>
|
||||
<link>http://metabar:8888/obidoc/docs/commands/options/</link>
|
||||
<description>Recent content in Shared command options on OBITools4 documentation</description>
|
||||
<generator>Hugo</generator>
|
||||
<language>en-us</language>
|
||||
<lastBuildDate></lastBuildDate>
|
||||
<atom:link href="http://metabar:8888/obidoc/docs/commands/options/index.xml" rel="self" type="application/rss+xml" />
|
||||
</channel>
|
||||
</rss>
|
||||
@@ -0,0 +1,6 @@
|
||||
>AB061527 {"count":1,"definition":"Sorex unguiculatus mitochondrial NA, complete genome.","family_name":"Soricidae","family_taxid":9376,"genus_name":"Sorex","genus_taxid":9379,"obicleandb_level":"family","obicleandb_trusted":2.2137847111025621e-13,"species_name":"Sorex unguiculatus","species_taxid":62275,"taxid":62275}
|
||||
ttagccctaaacttaggtatttaatctaacaaaaatacccgtcagagaactactagcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>AL355887 {"count":2,"definition":"Human chromosome 14 NA sequence BAC R-179O11 of library RPCI-11 from chromosome 14 of Homo sapiens (Human)XXKW HTG.; HTGS_ACTIVFIN.","family_name":"Hominidae","family_taxid":9604,"genus_name":"Homo","genus_taxid":9605,"obicleandb_level":"genus","obicleandb_trusted":0,"species_name":"Homo sapiens","species_taxid":9606,"taxid":9606}
|
||||
ttagccctaaactctagtagttacattaacaaaaccattcgtcagaatactacgagcaac
|
||||
agcttaaaactcaaaggacctggcagttctttatatccct
|
||||
File diff suppressed because it is too large.
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@@ -0,0 +1,12 @@
|
||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||
<channel>
|
||||
<title>Others on OBITools4 documentation</title>
|
||||
<link>http://metabar:8888/obidoc/docs/commands/others/</link>
|
||||
<description>Recent content in Others on OBITools4 documentation</description>
|
||||
<generator>Hugo</generator>
|
||||
<language>en-us</language>
|
||||
<lastBuildDate></lastBuildDate>
|
||||
<atom:link href="http://metabar:8888/obidoc/docs/commands/others/index.xml" rel="self" type="application/rss+xml" />
|
||||
</channel>
|
||||
</rss>
|
||||
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File diff suppressed because it is too large.
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@@ -0,0 +1,12 @@
|
||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||
<channel>
|
||||
<title>Taxonomy on OBITools4 documentation</title>
|
||||
<link>http://metabar:8888/obidoc/docs/commands/taxonomy/</link>
|
||||
<description>Recent content in Taxonomy on OBITools4 documentation</description>
|
||||
<generator>Hugo</generator>
|
||||
<language>en-us</language>
|
||||
<lastBuildDate></lastBuildDate>
|
||||
<atom:link href="http://metabar:8888/obidoc/docs/commands/taxonomy/index.xml" rel="self" type="application/rss+xml" />
|
||||
</channel>
|
||||
</rss>
|
||||
@@ -0,0 +1,604 @@
|
||||
#!/usr/bin/env python3
|
||||
|
||||
import re
|
||||
import gzip
|
||||
import struct
|
||||
import sys
|
||||
import time
|
||||
import getopt
|
||||
from functools import cmp_to_key
|
||||
|
||||
_dbenable=False
|
||||
|
||||
#####
|
||||
#
|
||||
#
|
||||
# Generic file function
|
||||
#
|
||||
#
|
||||
#####
|
||||
|
||||
def universalOpen(file):
|
||||
if isinstance(file,str):
|
||||
if file[-3:] == '.gz':
|
||||
rep = gzip.open(file)
|
||||
else:
|
||||
rep = open(file)
|
||||
else:
|
||||
rep = file
|
||||
return rep
|
||||
|
||||
def universalTell(file):
|
||||
if isinstance(file, gzip.GzipFile):
|
||||
file=file.myfileobj
|
||||
return file.tell()
|
||||
|
||||
def fileSize(file):
|
||||
if isinstance(file, gzip.GzipFile):
|
||||
file=file.myfileobj
|
||||
pos = file.tell()
|
||||
file.seek(0,2)
|
||||
length = file.tell()
|
||||
file.seek(pos,0)
|
||||
return length
|
||||
|
||||
def progressBar(pos,max,reset=False,delta=[]):
|
||||
if reset:
|
||||
del delta[:]
|
||||
if not delta:
|
||||
delta.append(time.time())
|
||||
delta.append(time.time())
|
||||
|
||||
delta[1]=time.time()
|
||||
elapsed = delta[1]-delta[0]
|
||||
percent = float(pos)/max * 100
|
||||
remain = time.strftime('%H:%M:%S',time.gmtime(elapsed / percent * (100-percent)))
|
||||
bar = '#' * int(percent/2)
|
||||
bar+= '|/-\\-'[pos % 5]
|
||||
bar+= ' ' * (50 - int(percent/2))
|
||||
sys.stderr.write('\r%5.1f %% |%s] remain : %s' %(percent,bar,remain))
|
||||
|
||||
#####
|
||||
#
|
||||
#
|
||||
# NCBI Dump Taxonomy reader
|
||||
#
|
||||
#
|
||||
#####
|
||||
|
||||
def endLessIterator(endedlist):
|
||||
for x in endedlist:
|
||||
yield x
|
||||
while(1):
|
||||
yield endedlist[-1]
|
||||
|
||||
class ColumnFile(object):
|
||||
|
||||
def __init__(self,stream,sep=None,strip=True,types=None):
|
||||
if isinstance(stream,str):
|
||||
self._stream = open(stream)
|
||||
else:
|
||||
try:
|
||||
iter(stream)
|
||||
self._stream = stream
|
||||
except TypeError:
|
||||
raise ValueError('stream must be string or an iterator')
|
||||
self._delimiter=sep
|
||||
self._strip=strip
|
||||
if types:
|
||||
self._types=[x for x in types]
|
||||
for i in range(len(self._types)):
|
||||
if self._types[i] is bool:
|
||||
self._types[i]=ColumnFile.str2bool
|
||||
else:
|
||||
self._types=None
|
||||
|
||||
def str2bool(x):
|
||||
return bool(eval(x.strip()[0].upper(),{'T':True,'V':True,'F':False}))
|
||||
|
||||
str2bool = staticmethod(str2bool)
|
||||
|
||||
|
||||
def __iter__(self):
|
||||
return self
|
||||
|
||||
def __next__(self):
|
||||
ligne = next(self._stream)
|
||||
data = ligne.split(self._delimiter)
|
||||
if self._strip or self._types:
|
||||
data = [x.strip() for x in data]
|
||||
if self._types:
|
||||
it = endLessIterator(self._types)
|
||||
data = [x[1](x[0]) for x in ((y,next(it)) for y in data)]
|
||||
return data
|
||||
|
||||
def taxonCmp(t1,t2):
|
||||
if t1[0] < t2[0]:
|
||||
return -1
|
||||
elif t1[0] > t2[0]:
|
||||
return +1
|
||||
return 0
|
||||
|
||||
def bsearchTaxon(taxonomy,taxid):
|
||||
taxCount = len(taxonomy)
|
||||
begin = 0
|
||||
end = taxCount
|
||||
oldcheck=taxCount
|
||||
check = int(begin + end / 2)
|
||||
while check != oldcheck and taxonomy[check][0]!=taxid :
|
||||
if taxonomy[check][0] < taxid:
|
||||
begin=check
|
||||
else:
|
||||
end=check
|
||||
oldcheck=check
|
||||
check = int((begin + end) / 2)
|
||||
|
||||
|
||||
if taxonomy[check][0]==taxid:
|
||||
return check
|
||||
else:
|
||||
return None
|
||||
|
||||
|
||||
|
||||
def readNodeTable(file):
|
||||
|
||||
file = universalOpen(file)
|
||||
|
||||
nodes = ColumnFile(file,
|
||||
sep='|',
|
||||
types=(int,int,str,
|
||||
str,str,bool,
|
||||
int,bool,int,
|
||||
bool,bool,bool,str))
|
||||
print("Reading taxonomy dump file...", file=sys.stderr)
|
||||
taxonomy=[[n[0],n[2],n[1]] for n in nodes]
|
||||
print("List all taxonomy rank...", file=sys.stderr)
|
||||
ranks =list(set(x[1] for x in taxonomy))
|
||||
ranks.sort()
|
||||
ranks = {rank: index for index, rank in enumerate(ranks)}
|
||||
|
||||
print("Sorting taxons...", file=sys.stderr)
|
||||
taxonomy.sort(key=lambda x: x[0])
|
||||
|
||||
print("Indexing taxonomy...", file=sys.stderr)
|
||||
index = {}
|
||||
for t in taxonomy:
|
||||
index[t[0]]=bsearchTaxon(taxonomy, t[0])
|
||||
|
||||
print("Indexing parent and rank...", file=sys.stderr)
|
||||
for t in taxonomy:
|
||||
t[1]=ranks[t[1]]
|
||||
t[2]=index[t[2]]
|
||||
|
||||
|
||||
return taxonomy,ranks,index
|
||||
|
||||
def nameIterator(file):
|
||||
file = universalOpen(file)
|
||||
names = ColumnFile(file,
|
||||
sep='|',
|
||||
types=(int,str,
|
||||
str,str))
|
||||
for taxid,name,unique,classname,white in names:
|
||||
yield taxid,name,classname
|
||||
|
||||
def mergedNodeIterator(file):
|
||||
file = universalOpen(file)
|
||||
merged = ColumnFile(file,
|
||||
sep='|',
|
||||
types=(int,int,str))
|
||||
for taxid,current,white in merged:
|
||||
yield taxid,current
|
||||
|
||||
def deletedNodeIterator(file):
|
||||
file = universalOpen(file)
|
||||
deleted = ColumnFile(file,
|
||||
sep='|',
|
||||
types=(int,str))
|
||||
for taxid,white in deleted:
|
||||
yield taxid
|
||||
|
||||
def readTaxonomyDump(taxdir):
|
||||
taxonomy,ranks,index = readNodeTable('%s/nodes.dmp' % taxdir)
|
||||
|
||||
print("Adding scientific name...", file=sys.stderr)
|
||||
|
||||
alternativeName=[]
|
||||
for taxid,name,classname in nameIterator('%s/names.dmp' % taxdir):
|
||||
alternativeName.append((name,classname,index[taxid]))
|
||||
if classname == 'scientific name':
|
||||
taxonomy[index[taxid]].append(name)
|
||||
|
||||
print("Adding taxid alias...", file=sys.stderr)
|
||||
for taxid,current in mergedNodeIterator('%s/merged.dmp' % taxdir):
|
||||
index[taxid]=index[current]
|
||||
|
||||
print("Adding deleted taxid...", file=sys.stderr)
|
||||
for taxid in deletedNodeIterator('%s/delnodes.dmp' % taxdir):
|
||||
index[taxid]=None
|
||||
|
||||
return taxonomy,ranks,alternativeName,index
|
||||
|
||||
#####
|
||||
#
|
||||
#
|
||||
# Genbank/EMBL sequence reader
|
||||
#
|
||||
#
|
||||
#####
|
||||
|
||||
def entryIterator(file):
|
||||
file = universalOpen(file)
|
||||
rep =[]
|
||||
ligne = file.readline()
|
||||
while ligne:
|
||||
rep.append(ligne)
|
||||
if ligne == '//\n':
|
||||
rep = ''.join(rep)
|
||||
yield rep
|
||||
rep = []
|
||||
ligne = file.readline()
|
||||
|
||||
def fastaEntryIterator(file):
|
||||
file = universalOpen(file)
|
||||
rep =[]
|
||||
ligne = file.readline()
|
||||
while ligne:
|
||||
if ligne[0] == '>' and rep:
|
||||
rep = ''.join(rep)
|
||||
yield rep
|
||||
rep = []
|
||||
rep.append(ligne)
|
||||
ligne = file.readline()
|
||||
|
||||
if rep:
|
||||
rep = ''.join(rep)
|
||||
yield rep
|
||||
|
||||
_cleanSeq = re.compile('[ \n0-9]+')
|
||||
|
||||
def cleanSeq(seq):
|
||||
return _cleanSeq.sub('',seq)
|
||||
|
||||
|
||||
_gbParseID = re.compile('(?<=^LOCUS {7})[^ ]+(?= )',re.MULTILINE)
|
||||
_gbParseDE = re.compile('(?<=^DEFINITION {2}).+?\\. *$(?=[^ ])',re.MULTILINE+re.DOTALL)
|
||||
_gbParseSQ = re.compile('(?<=^ORIGIN).+?(?=^//$)',re.MULTILINE+re.DOTALL)
|
||||
_gbParseTX = re.compile('(?<= /db_xref="taxon:)[0-9]+(?=")')
|
||||
|
||||
def genbankEntryParser(entry):
|
||||
Id = _gbParseID.findall(entry)[0]
|
||||
De = ' '.join(_gbParseDE.findall(entry)[0].split())
|
||||
Sq = cleanSeq(_gbParseSQ.findall(entry)[0].upper())
|
||||
try:
|
||||
Tx = int(_gbParseTX.findall(entry)[0])
|
||||
except IndexError:
|
||||
Tx = None
|
||||
return {'id':Id,'taxid':Tx,'definition':De,'sequence':Sq}
|
||||
|
||||
######################
|
||||
|
||||
_cleanDef = re.compile('[\nDE]')
|
||||
|
||||
def cleanDef(definition):
|
||||
return _cleanDef.sub('',definition)
|
||||
|
||||
_emblParseID = re.compile('(?<=^ID {3})[^ ]+(?=;)',re.MULTILINE)
|
||||
_emblParseDE = re.compile('(?<=^DE {3}).+?\\. *$(?=[^ ])',re.MULTILINE+re.DOTALL)
|
||||
_emblParseSQ = re.compile('(?<=^ ).+?(?=^//$)',re.MULTILINE+re.DOTALL)
|
||||
_emblParseTX = re.compile('(?<= /db_xref="taxon:)[0-9]+(?=")')
|
||||
|
||||
def emblEntryParser(entry):
|
||||
Id = _emblParseID.findall(entry)[0]
|
||||
De = ' '.join(cleanDef(_emblParseDE.findall(entry)[0]).split())
|
||||
Sq = cleanSeq(_emblParseSQ.findall(entry)[0].upper())
|
||||
try:
|
||||
Tx = int(_emblParseTX.findall(entry)[0])
|
||||
except IndexError:
|
||||
Tx = None
|
||||
return {'id':Id,'taxid':Tx,'definition':De,'sequence':Sq}
|
||||
|
||||
|
||||
######################
|
||||
|
||||
_fastaSplit=re.compile(';\\W*')
|
||||
|
||||
def parseFasta(seq):
|
||||
seq=seq.split('\n')
|
||||
title = seq[0].strip()[1:].split(None,1)
|
||||
id=title[0]
|
||||
if len(title) == 2:
|
||||
field = _fastaSplit.split(title[1])
|
||||
else:
|
||||
field=[]
|
||||
info = dict(x.split('=',1) for x in field if '=' in x)
|
||||
definition = ' '.join([x for x in field if '=' not in x])
|
||||
seq=(''.join([x.strip() for x in seq[1:]])).upper()
|
||||
return id,seq,definition,info
|
||||
|
||||
|
||||
def fastaEntryParser(entry):
|
||||
id,seq,definition,info = parseFasta(entry)
|
||||
Tx = info.get('taxid',None)
|
||||
if Tx is not None:
|
||||
match = re.search(r'taxon:(\d+)', Tx)
|
||||
if match:
|
||||
Tx = match.group(1)
|
||||
Tx=int(Tx)
|
||||
return {'id':id,'taxid':Tx,'definition':definition,'sequence':seq}
|
||||
|
||||
|
||||
def sequenceIteratorFactory(entryParser,entryIterator):
|
||||
def sequenceIterator(file):
|
||||
for entry in entryIterator(file):
|
||||
yield entryParser(entry)
|
||||
return sequenceIterator
|
||||
|
||||
|
||||
def taxonomyInfo(entry,connection):
|
||||
taxid = entry['taxid']
|
||||
curseur = connection.cursor()
|
||||
curseur.execute("""
|
||||
select taxid,species,genus,family,
|
||||
taxonomy.scientificName(taxid) as sn,
|
||||
taxonomy.scientificName(species) as species_sn,
|
||||
taxonomy.scientificName(genus) as genus_sn,
|
||||
taxonomy.scientificName(family) as family_sn
|
||||
from
|
||||
(
|
||||
select alias as taxid,
|
||||
taxonomy.getSpecies(alias) as species,
|
||||
taxonomy.getGenus(alias) as genus,
|
||||
taxonomy.getFamily(alias) as family
|
||||
from taxonomy.aliases
|
||||
where id=%d ) as tax
|
||||
""" % taxid)
|
||||
rep = curseur.fetchone()
|
||||
entry['current_taxid']=rep[0]
|
||||
entry['species']=rep[1]
|
||||
entry['genus']=rep[2]
|
||||
entry['family']=rep[3]
|
||||
entry['scientific_name']=rep[4]
|
||||
entry['species_sn']=rep[5]
|
||||
entry['genus_sn']=rep[6]
|
||||
entry['family_sn']=rep[7]
|
||||
return entry
|
||||
|
||||
#####
|
||||
#
|
||||
#
|
||||
# Binary writer
|
||||
#
|
||||
#
|
||||
#####
|
||||
|
||||
def ecoSeqPacker(sq):
|
||||
|
||||
compactseq = gzip.zlib.compress(bytes(sq['sequence'],"ascii"),9)
|
||||
cptseqlength = len(compactseq)
|
||||
delength = len(sq['definition'])
|
||||
|
||||
totalSize = 4 + 20 + 4 + 4 + 4 + cptseqlength + delength
|
||||
|
||||
packed = struct.pack('> I I 20s I I I %ds %ds' % (delength,cptseqlength),
|
||||
totalSize,
|
||||
sq['taxid'],
|
||||
bytes(sq['id'],"ascii"),
|
||||
delength,
|
||||
len(sq['sequence']),
|
||||
cptseqlength,
|
||||
bytes(sq['definition'],"ascii"),
|
||||
compactseq)
|
||||
|
||||
assert len(packed) == totalSize+4, "error in sequence packing"
|
||||
|
||||
return packed
|
||||
|
||||
def ecoTaxPacker(tx):
|
||||
|
||||
namelength = len(tx[3])
|
||||
|
||||
totalSize = 4 + 4 + 4 + 4 + namelength
|
||||
|
||||
packed = struct.pack('> I I I I I %ds' % namelength,
|
||||
totalSize,
|
||||
tx[0],
|
||||
tx[1],
|
||||
tx[2],
|
||||
namelength,
|
||||
bytes(tx[3],"ascii"))
|
||||
|
||||
return packed
|
||||
|
||||
def ecoRankPacker(rank):
|
||||
|
||||
namelength = len(rank)
|
||||
|
||||
packed = struct.pack('> I %ds' % namelength,
|
||||
namelength,
|
||||
bytes(rank, 'ascii'))
|
||||
|
||||
return packed
|
||||
|
||||
def ecoNamePacker(name):
|
||||
|
||||
namelength = len(name[0])
|
||||
classlength= len(name[1])
|
||||
totalSize = namelength + classlength + 4 + 4 + 4 + 4
|
||||
|
||||
packed = struct.pack('> I I I I I %ds %ds' % (namelength,classlength),
|
||||
totalSize,
|
||||
int(name[1]=='scientific name'),
|
||||
namelength,
|
||||
classlength,
|
||||
name[2],
|
||||
bytes(name[0], 'ascii'),
|
||||
bytes(name[1], 'ascii'))
|
||||
|
||||
return packed
|
||||
|
||||
def ecoSeqWriter(file,input,taxindex,parser):
|
||||
output = open(file,'wb')
|
||||
input = universalOpen(input)
|
||||
inputsize = fileSize(input)
|
||||
entries = parser(input)
|
||||
seqcount=0
|
||||
skipped = []
|
||||
|
||||
output.write(struct.pack('> I',seqcount))
|
||||
|
||||
progressBar(1, inputsize,reset=True)
|
||||
for entry in entries:
|
||||
if entry['taxid'] is not None:
|
||||
try:
|
||||
entry['taxid']=taxindex[entry['taxid']]
|
||||
except KeyError:
|
||||
entry['taxid']=None
|
||||
if entry['taxid'] is not None:
|
||||
seqcount+=1
|
||||
output.write(ecoSeqPacker(entry))
|
||||
else:
|
||||
skipped.append(entry['id'])
|
||||
where = universalTell(input)
|
||||
progressBar(where, inputsize)
|
||||
print(" Readed sequences : %d " % seqcount, end=' ', file=sys.stderr)
|
||||
else:
|
||||
skipped.append(entry['id'])
|
||||
|
||||
print(file=sys.stderr)
|
||||
output.seek(0,0)
|
||||
output.write(struct.pack('> I',seqcount))
|
||||
|
||||
output.close()
|
||||
return skipped
|
||||
|
||||
|
||||
def ecoTaxWriter(file,taxonomy):
|
||||
output = open(file,'wb')
|
||||
output.write(struct.pack('> I',len(taxonomy)))
|
||||
|
||||
for tx in taxonomy:
|
||||
output.write(ecoTaxPacker(tx))
|
||||
|
||||
output.close()
|
||||
|
||||
def ecoRankWriter(file,ranks):
|
||||
output = open(file,'wb')
|
||||
output.write(struct.pack('> I',len(ranks)))
|
||||
|
||||
rankNames = list(ranks.keys())
|
||||
rankNames.sort()
|
||||
|
||||
for rank in rankNames:
|
||||
output.write(ecoRankPacker(rank))
|
||||
|
||||
output.close()
|
||||
|
||||
def nameCmp(n1,n2):
|
||||
name1=n1[0].upper()
|
||||
name2=n2[0].upper()
|
||||
if name1 < name2:
|
||||
return -1
|
||||
elif name1 > name2:
|
||||
return 1
|
||||
return 0
|
||||
|
||||
|
||||
def ecoNameWriter(file,names):
|
||||
output = open(file,'wb')
|
||||
output.write(struct.pack('> I',len(names)))
|
||||
|
||||
names.sort(key=lambda x:x[0].upper())
|
||||
|
||||
for name in names:
|
||||
output.write(ecoNamePacker(name))
|
||||
|
||||
output.close()
|
||||
|
||||
def ecoDBWriter(prefix,taxonomy,seqFileNames,parser):
|
||||
|
||||
ecoRankWriter('%s.rdx' % prefix, taxonomy[1])
|
||||
ecoTaxWriter('%s.tdx' % prefix, taxonomy[0])
|
||||
ecoNameWriter('%s.ndx' % prefix, taxonomy[2])
|
||||
|
||||
filecount = 0
|
||||
for filename in seqFileNames:
|
||||
filecount+=1
|
||||
sk=ecoSeqWriter('%s_%03d.sdx' % (prefix,filecount),
|
||||
filename,
|
||||
taxonomy[3],
|
||||
parser)
|
||||
if sk:
|
||||
print("Skipped entry :", file=sys.stderr)
|
||||
print(sk, file=sys.stderr)
|
||||
|
||||
def ecoParseOptions(arguments):
|
||||
opt = {
|
||||
'prefix' : 'ecodb',
|
||||
'taxdir' : 'taxdump',
|
||||
'parser' : sequenceIteratorFactory(genbankEntryParser,
|
||||
entryIterator)
|
||||
}
|
||||
|
||||
o,filenames = getopt.getopt(arguments,
|
||||
'ht:T:n:gfe',
|
||||
['help',
|
||||
'taxonomy=',
|
||||
'taxonomy_db=',
|
||||
'name=',
|
||||
'genbank',
|
||||
'fasta',
|
||||
'embl'])
|
||||
|
||||
for name,value in o:
|
||||
if name in ('-h','--help'):
|
||||
printHelp()
|
||||
exit()
|
||||
elif name in ('-t','--taxonomy'):
|
||||
opt['taxmod']='dump'
|
||||
opt['taxdir']=value
|
||||
elif name in ('-T','--taxonomy_db'):
|
||||
opt['taxmod']='db'
|
||||
opt['taxdb']=value
|
||||
elif name in ('-n','--name'):
|
||||
opt['prefix']=value
|
||||
elif name in ('-g','--genbank'):
|
||||
opt['parser']=sequenceIteratorFactory(genbankEntryParser,
|
||||
entryIterator)
|
||||
|
||||
elif name in ('-f','--fasta'):
|
||||
opt['parser']=sequenceIteratorFactory(fastaEntryParser,
|
||||
fastaEntryIterator)
|
||||
|
||||
elif name in ('-e','--embl'):
|
||||
opt['parser']=sequenceIteratorFactory(emblEntryParser,
|
||||
entryIterator)
|
||||
else:
|
||||
raise ValueError('Unknown option %s' % name)
|
||||
|
||||
return opt,filenames
|
||||
|
||||
def printHelp():
|
||||
print("-----------------------------------")
|
||||
print(" ecoPCRFormat.py")
|
||||
print("-----------------------------------")
|
||||
print("ecoPCRFormat.py [option] <argument>")
|
||||
print("-----------------------------------")
|
||||
print("-e --embl :[E]mbl format")
|
||||
print("-f --fasta :[F]asta format")
|
||||
print("-g --genbank :[G]enbank format")
|
||||
print("-h --help :[H]elp - print this help")
|
||||
print("-n --name :[N]ame of the new database created")
|
||||
print("-t --taxonomy :[T]axonomy - path to the taxonomy database")
|
||||
print(" :bcp-like dump from GenBank taxonomy database.")
|
||||
print("-----------------------------------")
|
||||
|
||||
if __name__ == '__main__':
|
||||
|
||||
opt,filenames = ecoParseOptions(sys.argv[1:])
|
||||
|
||||
taxonomy = readTaxonomyDump(opt['taxdir'])
|
||||
|
||||
ecoDBWriter(opt['prefix'], taxonomy, filenames, opt['parser'])
|
||||
|
||||
File diff suppressed because it is too large.
Load diff
@@ -0,0 +1,11 @@
|
||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||
<channel>
|
||||
<title>Designing new barcodes on OBITools4 documentation</title>
|
||||
<link>http://metabar:8888/obidoc/docs/cookbook/ecoprimers/</link>
|
||||
<description>Recent content in Designing new barcodes on OBITools4 documentation</description>
|
||||
<generator>Hugo</generator>
|
||||
<language>en-us</language>
|
||||
<atom:link href="http://metabar:8888/obidoc/docs/cookbook/ecoprimers/index.xml" rel="self" type="application/rss+xml" />
|
||||
</channel>
|
||||
</rss>
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 168 KiB |
@@ -0,0 +1,103 @@
|
||||
SHELL := /bin/bash
|
||||
FTPNCBI=ftp.ncbi.nlm.nih.gov
|
||||
GBURL=https://$(FTPNCBI)/genbank
|
||||
GBRELEASE_URL=$(GBURL)/GB_Release_Number
|
||||
|
||||
TAXOURL=https://$(FTPNCBI)/pub/taxonomy/taxdump.tar.gz
|
||||
|
||||
GBRELEASE:=$(shell curl $(GBRELEASE_URL))
|
||||
|
||||
GBDIV_ALL:=$(shell curl -L ${GBURL} \
|
||||
| grep -E 'gb.+\.seq\.gz' \
|
||||
| sed -E 's@^.*<a href="gb([^0-9]+)[0-9]+\.seq.gz.*$$@\1@' \
|
||||
| sort \
|
||||
| uniq)
|
||||
|
||||
GBDIV=bct inv mam phg pln pri rod vrl vrt
|
||||
DIRECTORIES=fasta fasta_fgs
|
||||
|
||||
GBFILE_ALL:=$(shell curl -L ${GBURL} \
|
||||
| grep -E "gb($$(tr ' ' '|' <<< "${GBDIV}"))[0-9]+" \
|
||||
| sed -E 's@^<a href="(gb.+.seq.gz)">.*$$@\1@')
|
||||
|
||||
|
||||
SUFFIXES += .d
|
||||
NODEPS:=clean taxonomy
|
||||
DEPFILES:=$(wildcard Release_$(GBRELEASE)/depends/*.d)
|
||||
|
||||
ifeq (0, $(words $(findstring $(MAKECMDGOALS), $(NODEPS))))
|
||||
#Chances are, these files don't exist. GMake will create them and
|
||||
#clean up automatically afterwards
|
||||
-include $(DEPFILES)
|
||||
endif
|
||||
|
||||
|
||||
all: depends directories FORCE
|
||||
@make downloads
|
||||
|
||||
downloads: taxonomy fasta_files
|
||||
@echo Genbank Release number $(GBRELEASE)
|
||||
@echo all divisions : $(GBDIV_ALL)
|
||||
|
||||
FORCE:
|
||||
@sleep 1
|
||||
|
||||
.PHONY: all directories depends taxonomy fasta_files FORCE
|
||||
|
||||
depends: directories Release_$(GBRELEASE)/depends/gbfiles.d Makefile
|
||||
|
||||
division: $(GBDIV)
|
||||
|
||||
taxonomy: directories Release_$(GBRELEASE)/taxonomy
|
||||
|
||||
directories: Release_$(GBRELEASE)/fasta Release_$(GBRELEASE)/stamp Release_$(GBRELEASE)/tmp
|
||||
|
||||
Release_$(GBRELEASE):
|
||||
@mkdir -p $@
|
||||
@echo Create $@ directory
|
||||
|
||||
Release_$(GBRELEASE)/fasta: Release_$(GBRELEASE)
|
||||
@mkdir -p $@
|
||||
@echo Create $@ directory
|
||||
|
||||
Release_$(GBRELEASE)/stamp: Release_$(GBRELEASE)
|
||||
@mkdir -p $@
|
||||
@echo Create $@ directory
|
||||
|
||||
Release_$(GBRELEASE)/tmp: Release_$(GBRELEASE)
|
||||
@mkdir -p $@
|
||||
@echo Create $@ directory
|
||||
|
||||
Release_$(GBRELEASE)/depends/gbfiles.d: Makefile
|
||||
@echo Create depends directory
|
||||
@mkdir -p Release_$(GBRELEASE)/depends
|
||||
@for f in ${GBFILE_ALL} ; do \
|
||||
echo -e "Release_$(GBRELEASE)/stamp/$$f.stamp:" ; \
|
||||
echo -e "\t@echo Downloading file : $$f..." ; \
|
||||
echo -e "\t@mkdir -p Release_$(GBRELEASE)/tmp" ; \
|
||||
echo -e "\t@mkdir -p Release_$(GBRELEASE)/stamp" ; \
|
||||
echo -e "\t@curl -L ${GBURL}/$$f > Release_$(GBRELEASE)/tmp/$$f && touch \$$@" ; \
|
||||
echo ; \
|
||||
div=$$(sed -E 's@^gb(...).*$$@\1@' <<< $$f) ; \
|
||||
fasta="Release_$(GBRELEASE)/fasta/$$div/$${f/.seq.gz/.fasta.gz}" ; \
|
||||
fasta_fgs="Release_$(GBRELEASE)/fasta_fgs/$$div/$${f/.seq.gz/.fasta.gz}" ; \
|
||||
fasta_files="$$fasta_files $$fasta" ; \
|
||||
fasta_fgs_files="$$fasta_fgs_files $$fasta_fgs" ; \
|
||||
echo -e "$$fasta: Release_$(GBRELEASE)/stamp/$$f.stamp" ; \
|
||||
echo -e "\t@echo converting file : \$$< in fasta" ; \
|
||||
echo -e "\t@mkdir -p Release_$(GBRELEASE)/fasta/$$div" ; \
|
||||
echo -e "\t@obiconvert -Z --fasta-output --skip-empty \\" ; \
|
||||
echo -e "\t Release_$(GBRELEASE)/tmp/$$f > Release_$(GBRELEASE)/tmp/$${f/.seq.gz/.fasta.gz} \\" ; \
|
||||
echo -e "\t && mv Release_$(GBRELEASE)/tmp/$${f/.seq.gz/.fasta.gz} \$$@ \\" ; \
|
||||
echo -e "\t && rm -f Release_$(GBRELEASE)/tmp/$$f \\" ; \
|
||||
echo -e "\t || rm -f \$$@" ; \
|
||||
echo -e "\t@echo conversion of $$@ done." ; \
|
||||
echo ; \
|
||||
done > $@ ; \
|
||||
echo >> $@ ; \
|
||||
echo "fasta_files: $$fasta_files" >> $@ ;
|
||||
|
||||
Release_$(GBRELEASE)/taxonomy:
|
||||
mkdir -p $@
|
||||
curl -iL $(TAXOURL) \
|
||||
| tar -C $@ -zxf -
|
||||
File diff suppressed because it is too large.
Load diff
@@ -0,0 +1,11 @@
|
||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||
<channel>
|
||||
<title>Analysing an Illumina data set on OBITools4 documentation</title>
|
||||
<link>http://metabar:8888/obidoc/docs/cookbook/illumina/</link>
|
||||
<description>Recent content in Analysing an Illumina data set on OBITools4 documentation</description>
|
||||
<generator>Hugo</generator>
|
||||
<language>en-us</language>
|
||||
<atom:link href="http://metabar:8888/obidoc/docs/cookbook/illumina/index.xml" rel="self" type="application/rss+xml" />
|
||||
</channel>
|
||||
</rss>
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 16 KiB |
File diff suppressed because it is too large.
Load diff
+26
@@ -0,0 +1,26 @@
|
||||
>HELIUM_000100422_612GNAAXX:7:118:3572:14633#0/1_sub[28..126] {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:99:9351:13090#0/1_sub[28..127] {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337}}
|
||||
ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:108:10111:9078#0/1_sub[28..127] {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039}}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:38:14204:12725#0/1_sub[28..126] {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:98:16207:5869#0/1_sub[78..81] {"count":2007,"merged_sample":{"29a_F260619":2007},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":2021}}
|
||||
tttt
|
||||
>HELIUM_000100422_612GNAAXX:7:30:9942:4495#0/1_sub[28..126] {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105}}
|
||||
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
|
||||
gattaaacctcaaaggacttggcagtgctttatacccct
|
||||
>HELIUM_000100422_612GNAAXX:7:51:16702:19393#0/1_sub[28..127] {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_head":true,"obiclean_headcount":2,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":0,"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127] {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376}}
|
||||
ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126] {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":4,"obiclean_singletoncount":3,"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1}}
|
||||
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
+5864
File diff suppressed because it is too large.
Load diff
+2140
File diff suppressed because it is too large.
Load diff
+24
@@ -0,0 +1,24 @@
|
||||
>HELIUM_000100422_612GNAAXX:7:118:3572:14633#0/1_sub[28..126] {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:99:9351:13090#0/1_sub[28..127] {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337}}
|
||||
ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:108:10111:9078#0/1_sub[28..127] {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039}}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:38:14204:12725#0/1_sub[28..126] {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:30:9942:4495#0/1_sub[28..126] {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105}}
|
||||
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
|
||||
gattaaacctcaaaggacttggcagtgctttatacccct
|
||||
>HELIUM_000100422_612GNAAXX:7:51:16702:19393#0/1_sub[28..127] {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_head":true,"obiclean_headcount":2,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":0,"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127] {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376}}
|
||||
ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126] {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":4,"obiclean_singletoncount":3,"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1}}
|
||||
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
+329
@@ -0,0 +1,329 @@
|
||||
>HELIUM_000100422_612GNAAXX:7:56:19300:10949#0/1_sub[28..127] {"count":37,"merged_sample":{"29a_F260619":37},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":43}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattgttcaccagagtactagcggcaac
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:63:4595:15643#0/1_sub[28..126] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":4}}
|
||||
ttagccctaaacataagctattccataacaaaataattcgccagagtactaccggcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:7:8807:7823#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":3}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtcataccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:108:19171:11413#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":1,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":1,"obiclean_mutation":{"HELIUM_000100422_612GNAAXX:7:8:6794:4925#0/1_sub[28..127]":"(t)->(g)@38"},"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"i","29a_F260619":"s"},"obiclean_weight":{"15a_F730814":1,"29a_F260619":1}}
|
||||
ttagccctaaacacaagtaattaatataacaaaagtagtcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:44:5008:2115#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
|
||||
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:53:16956:10563#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":4}}
|
||||
ttagccctaaacataaacattcaataaacaaggatgttcgcaagagtactactagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:54:10323:7022#0/1_sub[28..127] {"count":3,"merged_sample":{"13a_F730603":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":7}}
|
||||
ttagccctaaacacaaataattatataaacaaaactattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:45:7460:13396#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":3}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttatgcccgt
|
||||
>HELIUM_000100422_612GNAAXX:7:58:8409:9911#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
|
||||
ttagccctaaacataaacattcaataaacaaaataattcgccagaggactactagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:118:3572:14633#0/1_sub[28..126] {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:100:18844:15930#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":2}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaagcgcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:29:9723:20435#0/1_sub[28..127] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":4}}
|
||||
ttagccctaaacacaaataattacacaaacaaaattgttcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:43:4660:16319#0/1_sub[28..126] {"count":22,"merged_sample":{"26a_F040644":22},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":42}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:103:11045:3860#0/1_sub[28..127] {"count":4,"merged_sample":{"15a_F730814":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":4}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaagggcttggcggtgctttatgccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:67:10944:19430#0/1_sub[28..127] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":3}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgtcagagtactaccggcaat
|
||||
agcttaaaactcaaaggacgtggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:56:6962:17278#0/1_sub[28..126] {"count":4,"merged_sample":{"26a_F040644":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":7}}
|
||||
ttagccctaaacataaacattcaataaacaaaataattcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:60:13553:20530#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":1,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":2,"obiclean_status":{"15a_F730814":"s","29a_F260619":"s"},"obiclean_weight":{"15a_F730814":1,"29a_F260619":1}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||
atgttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:35:13167:18371#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccggagaactactaggaaca
|
||||
gcttaaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:105:1895:7593#0/1_sub[28..127] {"count":11,"merged_sample":{"29a_F260619":11},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":13}}
|
||||
ttagccctaaacctcaacagttaaatcaacaaaactgctcgccagaacactacgagccac
|
||||
agcttaaaactcaaaggacctggcggtgcttcatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:118:15661:12736#0/1_sub[28..127] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":2}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattatccgcaagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:30:8391:13152#0/1_sub[28..127] {"count":17,"merged_sample":{"13a_F730603":17},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":25}}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaac
|
||||
agcccaaaactcaaaggacttggcggtgcttcacaccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:95:14375:10838#0/1_sub[28..127] {"count":4,"merged_sample":{"29a_F260619":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":5}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcagtgctttatacccct
|
||||
>HELIUM_000100422_612GNAAXX:7:82:13334:18499#0/1_sub[28..127] {"count":6,"merged_sample":{"29a_F260619":6},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":10}}
|
||||
ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:108:11272:1128#0/1_sub[28..127] {"count":2,"merged_sample":{"13a_F730603":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":2}}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactactagcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:7:6016:14767#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":4}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtacgtctagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:99:9351:13090#0/1_sub[28..127] {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337}}
|
||||
ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:9:8337:12329#0/1_sub[28..126] {"count":5,"merged_sample":{"26a_F040644":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":6}}
|
||||
ttagccctaaacataaacagtcaataaacaaggatgttcgccagagtactactagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:15:12854:18952#0/1_sub[28..126] {"count":10,"merged_sample":{"29a_F260619":10},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":16}}
|
||||
ttagccctaaacataagctattccataacaaaattattcgccagagtactaccggcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:1:4513:20277#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
|
||||
ttagccctaaacataaaccattctataacaaaataattcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:57:18237:6765#0/1_sub[28..127] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":3}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattatgcgccagagtactgccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:108:10111:9078#0/1_sub[28..127] {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039}}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:119:8691:15994#0/1_sub[28..127] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":2}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcgat
|
||||
agcttaaaacgcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:6:1739:11421#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgctagagtactactagcaaca
|
||||
gcctgacactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:73:17136:17728#0/1_sub[28..127] {"count":6,"merged_sample":{"13a_F730603":6},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":7}}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaattattcgccagagtactaccggcaac
|
||||
agcccaaaactcaaaggacttggcggtgcttcacaccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:76:9874:3117#0/1_sub[28..127] {"count":9,"merged_sample":{"29a_F260619":9},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":12}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactagcggcaac
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:38:14204:12725#0/1_sub[28..126] {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:18:16679:15889#0/1_sub[28..127] {"count":4,"merged_sample":{"29a_F260619":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":4}}
|
||||
ttagccctaaacctcaacagttaaatcaacaaaactgctcgccagaacactacgagccac
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:52:6908:8410#0/1_sub[28..126] {"count":5,"merged_sample":{"26a_F040644":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":10}}
|
||||
ttagccctaaacataagctattctataacaaaataattcgccagagaactactagcaaca
|
||||
gcttaaaactcaaaggacttggcggtgctttatacccct
|
||||
>HELIUM_000100422_612GNAAXX:7:71:13461:7411#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":3}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagaagactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:98:16207:5869#0/1_sub[78..81] {"count":2007,"merged_sample":{"29a_F260619":2007},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":2021}}
|
||||
tttt
|
||||
>HELIUM_000100422_612GNAAXX:7:47:6989:13864#0/1_sub[28..126] {"count":3,"merged_sample":{"26a_F040644":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
|
||||
ttagccctaaacataaaccattctataacaaaataattcgccagagaactactagcaaca
|
||||
gcttaaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:72:8941:18482#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaatg
|
||||
gcctaaaactcaaaggacttggtggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:25:10818:13742#0/1_sub[28..133] {"count":8,"merged_sample":{"26a_F040644":8},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":8}}
|
||||
ttagccctaaacgtaaactgcaaactattccataataaaataattcgcccaagaactact
|
||||
agcaacagcttaaaactcaaaggacttggtggtgctttctacccct
|
||||
>HELIUM_000100422_612GNAAXX:7:70:11509:6042#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":2}}
|
||||
ttagccctaaacacaagaaattaatataacaaaaatattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:30:9942:4495#0/1_sub[28..126] {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105}}
|
||||
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
|
||||
gattaaacctcaaaggacttggcagtgctttatacccct
|
||||
>HELIUM_000100422_612GNAAXX:7:46:4342:17317#0/1_sub[28..126] {"count":5,"merged_sample":{"26a_F040644":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":8}}
|
||||
ttagccctaaacataaatcattctataacaaaataattcgccggagaactactaggaaca
|
||||
gcttaaaactcaaaggacttggcggtgccttacgtccct
|
||||
>HELIUM_000100422_612GNAAXX:7:111:17844:17230#0/1_sub[28..126] {"count":13,"merged_sample":{"26a_F040644":13},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":17}}
|
||||
ttagccctaaacataaatcagtctataacaaaataattcgccagagaactactagcaaca
|
||||
gcttaaaactcaaaggacgtggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:34:17680:16952#0/1_sub[28..127] {"count":15,"merged_sample":{"13a_F730603":15},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":15}}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgcttcacaccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:34:2640:2539#0/1_sub[28..127] {"count":19,"merged_sample":{"29a_F260619":19},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":25}}
|
||||
ttagccctaaacacaaataattacacaaacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:71:18891:9661#0/1_sub[28..126] {"count":3,"merged_sample":{"26a_F040644":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
|
||||
ttagccctaaacataaatcagtctataacaaaataattcgccagagaactactagcaaca
|
||||
gcttaaaactcaaaggacgtggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:26:16553:1613#0/1_sub[77..81] {"count":38,"merged_sample":{"13a_F730603":38},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":38}}
|
||||
caata
|
||||
>HELIUM_000100422_612GNAAXX:7:45:5732:11220#0/1_sub[28..126] {"count":3,"merged_sample":{"26a_F040644":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||
gcctgaaactcaaaggacttggtggtgctttctacccct
|
||||
>HELIUM_000100422_612GNAAXX:7:1:14254:1103#0/1_sub[28..126] {"count":8,"merged_sample":{"26a_F040644":8},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":11}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||
gcttaaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:50:17151:20608#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
|
||||
ttagccctaaacataaacattcaataaacaaaataattcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:96:13203:2879#0/1_sub[28..127] {"count":5,"merged_sample":{"13a_F730603":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":6}}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaac
|
||||
agcccaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:78:18041:18996#0/1_sub[28..126] {"count":13,"merged_sample":{"13a_F730603":9,"15a_F730814":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":2,"obiclean_status":{"13a_F730603":"s","15a_F730814":"s"},"obiclean_weight":{"13a_F730603":9,"15a_F730814":4}}
|
||||
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:80:18387:10166#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":1,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":1,"obiclean_mutation":{"HELIUM_000100422_612GNAAXX:7:100:14685:15065#0/1_sub[28..127]":"(a)->(t)@24","HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127]":"(t)->(g)@71"},"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s","29a_F260619":"i"},"obiclean_weight":{"15a_F730814":1,"29a_F260619":1}}
|
||||
ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaacgcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:54:10113:12172#0/1_sub[28..127] {"count":7,"merged_sample":{"15a_F730814":4,"29a_F260619":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":2,"obiclean_status":{"15a_F730814":"s","29a_F260619":"s"},"obiclean_weight":{"15a_F730814":5,"29a_F260619":4}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:97:17822:18365#0/1_sub[28..127] {"count":3,"merged_sample":{"29a_F260619":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":4}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactgccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttatcccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:87:6328:12406#0/1_sub[28..126] {"count":6,"merged_sample":{"26a_F040644":6},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":8}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||
gcctgaaactcaaaggacttggcagtgctttatacccct
|
||||
>HELIUM_000100422_612GNAAXX:7:7:4611:13145#0/1_sub[28..127] {"count":3,"merged_sample":{"13a_F730603":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":4}}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtacgtccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:51:16702:19393#0/1_sub[28..127] {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_head":true,"obiclean_headcount":2,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":0,"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:78:6346:5817#0/1_sub[28..127] {"count":5,"merged_sample":{"13a_F730603":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":5}}
|
||||
ttagccctaaacacaaataattatataaacaaaattattcgccagagtactaccggcaac
|
||||
agcccaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:7:15122:17310#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":1,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":1,"obiclean_mutation":{"HELIUM_000100422_612GNAAXX:7:94:6384:20392#0/1_sub[28..127]":"(a)->(t)@52"},"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"i","29a_F260619":"s"},"obiclean_weight":{"15a_F730814":1,"29a_F260619":1}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtacttcctgcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:27:7695:17738#0/1_sub[28..126] {"count":7,"merged_sample":{"26a_F040644":7},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":11}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:48:15379:13773#0/1_sub[28..126] {"count":5,"merged_sample":{"26a_F040644":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":5}}
|
||||
ttagccctaaacatagataattttacaacaagaatgttcgccagagtactactagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:117:16246:17184#0/1_sub[28..127] {"count":5,"merged_sample":{"13a_F730603":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":10}}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagaggactactagcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:87:11044:6323#0/1_sub[28..126] {"count":69,"merged_sample":{"26a_F040644":69},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":84}}
|
||||
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:40:12248:18615#0/1_sub[28..126] {"count":4,"merged_sample":{"26a_F040644":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":4}}
|
||||
ttagccctaaacataagctattctataacaaaataattcgccagagaactactagcaaca
|
||||
gcttaaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:7:6470:13562#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":2}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtacctccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:72:11850:15705#0/1_sub[28..126] {"count":4,"merged_sample":{"26a_F040644":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":4}}
|
||||
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:82:8566:4827#0/1_sub[28..126] {"count":6,"merged_sample":{"26a_F040644":6},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":9}}
|
||||
ttagccctaaacataaacattcaataaacaaggatgttcgcaagagtactactagcaatg
|
||||
gcctaaaactcaaaggacttggtggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:43:16297:17399#0/1_sub[28..127] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":3}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattgttcaccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:7:15117:2564#0/1_sub[28..127] {"count":2,"merged_sample":{"13a_F730603":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":2}}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtacctccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:90:4058:17862#0/1_sub[28..127] {"count":4,"merged_sample":{"13a_F730603":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":5}}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagaggactactagcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:43:13909:1377#0/1_sub[28..126] {"count":10,"merged_sample":{"26a_F040644":10},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":14}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaatg
|
||||
gcctaaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:36:3584:21256#0/1_sub[28..127] {"count":2,"merged_sample":{"13a_F730603":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":2}}
|
||||
ctagccttaaacacaaatagttatgcaaacaaagctattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttatgccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:80:13357:2959#0/1_sub[74..81] {"count":12,"merged_sample":{"29a_F260619":12},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":12}}
|
||||
ccgatagg
|
||||
>HELIUM_000100422_612GNAAXX:7:70:8097:4516#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
|
||||
ttagccctaaacataaacattcaagaaacaagaatgttcaccagagtactactagcaatg
|
||||
gcctaaaactcaaaggacttggcagtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:7:8746:5790#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtacctctagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:8:9165:18915#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactatgaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:85:7323:6139#0/1_sub[28..126] {"count":9,"merged_sample":{"26a_F040644":9},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":16}}
|
||||
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:23:6103:3418#0/1_sub[28..126] {"count":3,"merged_sample":{"26a_F040644":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":4}}
|
||||
ttagccctaaacatagataattttacaacaaaataattcgccagagtactactagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:107:2103:10677#0/1_sub[28..127] {"count":20,"merged_sample":{"13a_F730603":20},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":22}}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:1:15993:20360#0/1_sub[28..127] {"count":4,"merged_sample":{"13a_F730603":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":4}}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactacctgcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttatgccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:103:1205:6990#0/1_sub[28..127] {"count":2,"merged_sample":{"13a_F730603":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":2}}
|
||||
ttagccctaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:111:2380:10482#0/1_sub[28..126] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":2}}
|
||||
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:76:10530:11312#0/1_sub[28..126] {"count":43,"merged_sample":{"26a_F040644":43},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":69}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:40:15984:4911#0/1_sub[28..126] {"count":16,"merged_sample":{"26a_F040644":16},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":30}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:109:19171:17424#0/1_sub[28..126] {"count":2,"merged_sample":{"13a_F730603":1,"26a_F040644":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":1,"obiclean_mutation":{"HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126]":"(a)->(t)@51"},"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s","26a_F040644":"i"},"obiclean_weight":{"13a_F730603":1,"26a_F040644":1}}
|
||||
ttagccctaaacatagataattttacaacaaaataattcgccagaggacttctagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:77:17898:19592#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":1,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":2,"obiclean_status":{"15a_F730814":"s","29a_F260619":"s"},"obiclean_weight":{"15a_F730814":1,"29a_F260619":1}}
|
||||
ttagccctaaacacaagtaattaatataacaaaataattcgccagaggactactagcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:32:4908:16517#0/1_sub[78..81] {"count":7,"merged_sample":{"29a_F260619":7},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":7}}
|
||||
ccgc
|
||||
>HELIUM_000100422_612GNAAXX:7:100:8022:19461#0/1_sub[28..127] {"count":5,"merged_sample":{"29a_F260619":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":11}}
|
||||
ttagccctaaacacaagtaattaatataacaaaataattcgccagagaactactagcaac
|
||||
agattaaacctcaaaggacttggcagtgctttatacccct
|
||||
>HELIUM_000100422_612GNAAXX:7:59:2390:15297#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
|
||||
ttagccctaaacataaacattcaataaacaaggatgttcgcaagagtactactagcaatg
|
||||
gcctaaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:98:10839:20244#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
|
||||
ttagccctaaacataaacattcaataaacaaggatgttcgccagagtactactagcaatg
|
||||
gcctaaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:34:13086:6440#0/1_sub[28..127] {"count":14,"merged_sample":{"13a_F730603":14},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":18}}
|
||||
ttagccctaaacacaaataattatataaacaaaattattcgccagagtactaccggcaac
|
||||
agcccaaaactcaaaggacttggcggtgcttcacaccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:73:10944:14101#0/1_sub[28..127] {"count":2,"merged_sample":{"13a_F730603":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":3}}
|
||||
ttagccctaaacacaaataattatataaacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:61:17561:21218#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
|
||||
ttagccctaaacataaatcattctataacaaaataattcgccggagaactactaggaaca
|
||||
gcttaaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:93:7569:17305#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
|
||||
ttagccctaaacataaatcagtctataacaaaataattcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:55:11954:15731#0/1_sub[28..126] {"count":6,"merged_sample":{"29a_F260619":6},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":7}}
|
||||
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
|
||||
gattaaacctcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127] {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376}}
|
||||
ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:54:15067:12524#0/1_sub[28..126] {"count":26,"merged_sample":{"26a_F040644":26},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":49}}
|
||||
ttagccctaaacatagataattttacaacaaaataattcgccagagtactactagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:6:10451:2548#0/1_sub[28..126] {"count":12,"merged_sample":{"26a_F040644":12},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":15}}
|
||||
ttagccctaaacataaacagtcaataaacaaggatgttcgccagagtactactagcaatg
|
||||
gcctaaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:23:10872:20213#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
|
||||
ttagccctaaacataaatcattctataacaaaataattcgccggagaactactagcaaca
|
||||
gcttaaaactcaaaggacttggcggtgccttacgtccct
|
||||
>HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126] {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":4,"obiclean_singletoncount":3,"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1}}
|
||||
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:98:6034:5203#0/1_sub[28..127] {"count":3,"merged_sample":{"29a_F260619":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":4}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcaccagagtactagcggcaac
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:70:2429:19509#0/1_sub[28..126] {"count":5,"merged_sample":{"26a_F040644":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":5}}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgccttacgtccct
|
||||
>HELIUM_000100422_612GNAAXX:7:65:1843:2567#0/1_sub[28..126] {"count":7,"merged_sample":{"26a_F040644":7},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":11}}
|
||||
ttagccctaaacataaaccattctataacaaaataattcgccagagaactactagcaaca
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:92:1339:19811#0/1_sub[28..127] {"count":3,"merged_sample":{"29a_F260619":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":3}}
|
||||
ttagccctaaacacaagtaattacacaaacaaaattgttcacaagagtactagcggcaac
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:15:13855:1746#0/1_sub[28..127] {"count":3,"merged_sample":{"15a_F730814":2,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":1,"obiclean_mutation":{"HELIUM_000100422_612GNAAXX:7:7:14405:19348#0/1_sub[28..127]":"(t)->(g)@51"},"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s","29a_F260619":"i"},"obiclean_weight":{"15a_F730814":3,"29a_F260619":1}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtgcgaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:7:7092:11003#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":2}}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtacgtccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
+24
@@ -0,0 +1,24 @@
|
||||
>HELIUM_000100422_612GNAAXX:7:118:3572:14633#0/1_sub[28..126] {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205},"obitag_bestid":0.9797979797979798,"obitag_bestmatch":"AY227529","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","taxid":"taxon:9992 [Marmota]@genus"}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:99:9351:13090#0/1_sub[28..127] {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337},"obitag_bestid":0.9405940594059405,"obitag_bestmatch":"AF154263","obitag_match_count":9,"obitag_rank":"infraorder","obitag_similarity_method":"lcs","taxid":"taxon:35500 [Pecora]@infraorder"}
|
||||
ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:108:10111:9078#0/1_sub[28..127] {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039},"obitag_bestid":1,"obitag_bestmatch":"AB245427","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9860 [Cervus elaphus]@species"}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:38:14204:12725#0/1_sub[28..126] {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202},"obitag_bestid":0.9494949494949495,"obitag_bestmatch":"AY227530","obitag_match_count":2,"obitag_rank":"tribe","obitag_similarity_method":"lcs","taxid":"taxon:337730 [Marmotini]@tribe"}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:30:9942:4495#0/1_sub[28..126] {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105},"obitag_bestid":0.9595959595959596,"obitag_bestmatch":"AC187326","obitag_match_count":1,"obitag_rank":"subspecies","obitag_similarity_method":"lcs","taxid":"taxon:9615 [Canis lupus familiaris]@subspecies"}
|
||||
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
|
||||
gattaaacctcaaaggacttggcagtgctttatacccct
|
||||
>HELIUM_000100422_612GNAAXX:7:51:16702:19393#0/1_sub[28..127] {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_head":true,"obiclean_headcount":2,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":0,"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789},"obitag_bestid":1,"obitag_bestmatch":"AJ885202","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9858 [Capreolus capreolus]@species"}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127] {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376},"obitag_bestid":1,"obitag_bestmatch":"AJ972683","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9858 [Capreolus capreolus]@species"}
|
||||
ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126] {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":4,"obiclean_singletoncount":3,"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1},"obitag_bestid":1,"obitag_bestmatch":"AB048590","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","taxid":"taxon:9611 [Canis]@genus"}
|
||||
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
@@ -0,0 +1,24 @@
|
||||
>seq0001 {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205},"obitag_bestid":0.9797979797979798,"obitag_bestmatch":"AY227529","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","seq_number":1,"taxid":"taxon:9992 [Marmota]@genus"}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>seq0002 {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337},"obitag_bestid":0.9405940594059405,"obitag_bestmatch":"AF154263","obitag_match_count":9,"obitag_rank":"infraorder","obitag_similarity_method":"lcs","seq_number":2,"taxid":"taxon:35500 [Pecora]@infraorder"}
|
||||
ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>seq0003 {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039},"obitag_bestid":1,"obitag_bestmatch":"AB245427","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","seq_number":3,"taxid":"taxon:9860 [Cervus elaphus]@species"}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>seq0004 {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202},"obitag_bestid":0.9494949494949495,"obitag_bestmatch":"AY227530","obitag_match_count":2,"obitag_rank":"tribe","obitag_similarity_method":"lcs","seq_number":4,"taxid":"taxon:337730 [Marmotini]@tribe"}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>seq0005 {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105},"obitag_bestid":0.9595959595959596,"obitag_bestmatch":"AC187326","obitag_match_count":1,"obitag_rank":"subspecies","obitag_similarity_method":"lcs","seq_number":5,"taxid":"taxon:9615 [Canis lupus familiaris]@subspecies"}
|
||||
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
|
||||
gattaaacctcaaaggacttggcagtgctttatacccct
|
||||
>seq0006 {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789},"obitag_bestid":1,"obitag_bestmatch":"AJ885202","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","seq_number":6,"taxid":"taxon:9858 [Capreolus capreolus]@species"}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>seq0007 {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376},"obitag_bestid":1,"obitag_bestmatch":"AJ972683","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","seq_number":7,"taxid":"taxon:9858 [Capreolus capreolus]@species"}
|
||||
ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>seq0008 {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1},"obitag_bestid":1,"obitag_bestmatch":"AB048590","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","seq_number":8,"taxid":"taxon:9611 [Canis]@genus"}
|
||||
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
@@ -0,0 +1,9 @@
|
||||
id,count,obitag_bestid,obitag_bestmatch,obitag_match_count,obitag_rank,obitag_similarity_method,seq_number,taxid,sequence
|
||||
seq0001,10172,0.9797979797979798,AY227529,1,genus,lcs,1,taxon:9992 [Marmota]@genus,ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaacagcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
seq0002,260,0.9405940594059405,AF154263,9,infraorder,lcs,2,taxon:35500 [Pecora]@infraorder,ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaacagcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
seq0003,7146,1,AB245427,1,species,lcs,3,taxon:9860 [Cervus elaphus]@species,ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
seq0004,87,0.9494949494949495,AY227530,2,tribe,lcs,4,taxon:337730 [Marmotini]@tribe,ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaatagcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
seq0005,95,0.9595959595959596,AC187326,1,subspecies,lcs,5,taxon:9615 [Canis lupus familiaris]@subspecies,ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaacagattaaacctcaaaggacttggcagtgctttatacccct
|
||||
seq0006,12004,1,AJ885202,1,species,lcs,6,taxon:9858 [Capreolus capreolus]@species,ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
seq0007,319,1,AJ972683,1,species,lcs,7,taxon:9858 [Capreolus capreolus]@species,ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
seq0008,366,1,AB048590,1,genus,lcs,8,taxon:9611 [Canis]@genus,ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaatagcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
|
@@ -0,0 +1,6 @@
|
||||
id,seq0001,seq0002,seq0003,seq0004,seq0005,seq0006,seq0007,seq0008
|
||||
29a_F260619,0,337,0,0,105,5789,376,1
|
||||
15a_F730814,0,0,0,0,0,8822,0,5
|
||||
13a_F730603,0,0,8039,0,0,0,0,17
|
||||
26a_F040644,12205,0,0,202,12,0,0,468
|
||||
|
||||
|
@@ -0,0 +1,24 @@
|
||||
>HELIUM_000100422_612GNAAXX:7:118:3572:14633#0/1_sub[28..126] {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205},"obitag_bestid":0.9797979797979798,"obitag_bestmatch":"AY227529","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","taxid":"taxon:9992 [Marmota]@genus"}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:99:9351:13090#0/1_sub[28..127] {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337},"obitag_bestid":0.9405940594059405,"obitag_bestmatch":"AF154263","obitag_match_count":9,"obitag_rank":"infraorder","obitag_similarity_method":"lcs","taxid":"taxon:35500 [Pecora]@infraorder"}
|
||||
ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:108:10111:9078#0/1_sub[28..127] {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039},"obitag_bestid":1,"obitag_bestmatch":"AB245427","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9860 [Cervus elaphus]@species"}
|
||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:38:14204:12725#0/1_sub[28..126] {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202},"obitag_bestid":0.9494949494949495,"obitag_bestmatch":"AY227530","obitag_match_count":2,"obitag_rank":"tribe","obitag_similarity_method":"lcs","taxid":"taxon:337730 [Marmotini]@tribe"}
|
||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>HELIUM_000100422_612GNAAXX:7:30:9942:4495#0/1_sub[28..126] {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105},"obitag_bestid":0.9595959595959596,"obitag_bestmatch":"AC187326","obitag_match_count":1,"obitag_rank":"subspecies","obitag_similarity_method":"lcs","taxid":"taxon:9615 [Canis lupus familiaris]@subspecies"}
|
||||
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
|
||||
gattaaacctcaaaggacttggcagtgctttatacccct
|
||||
>HELIUM_000100422_612GNAAXX:7:51:16702:19393#0/1_sub[28..127] {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789},"obitag_bestid":1,"obitag_bestmatch":"AJ885202","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9858 [Capreolus capreolus]@species"}
|
||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127] {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376},"obitag_bestid":1,"obitag_bestmatch":"AJ972683","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9858 [Capreolus capreolus]@species"}
|
||||
ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
||||
>HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126] {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1},"obitag_bestid":1,"obitag_bestmatch":"AB048590","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","taxid":"taxon:9611 [Canis]@genus"}
|
||||
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
|
||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
Binary file not shown.
|
After Width: | Height: | Size: 17 KiB |
Binary file not shown.
@@ -0,0 +1,8 @@
|
||||
@param,matching,strict
|
||||
@param,primer_mismatches,2
|
||||
@param,indels,false
|
||||
experiment,sample,sample_tag,forward_primer,reverse_primer
|
||||
wolf_diet,13a_F730603,aattaac,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
|
||||
wolf_diet,15a_F730814,gaagtag,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
|
||||
wolf_diet,26a_F040644,gaatatc,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
|
||||
wolf_diet,29a_F260619,gcctcct,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
|
||||
|
File diff suppressed because it is too large.
Load diff
@@ -0,0 +1,12 @@
|
||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||
<channel>
|
||||
<title>Cookbook on OBITools4 documentation</title>
|
||||
<link>http://metabar:8888/obidoc/docs/cookbook/</link>
|
||||
<description>Recent content in Cookbook on OBITools4 documentation</description>
|
||||
<generator>Hugo</generator>
|
||||
<language>en-us</language>
|
||||
<lastBuildDate></lastBuildDate>
|
||||
<atom:link href="http://metabar:8888/obidoc/docs/cookbook/index.xml" rel="self" type="application/rss+xml" />
|
||||
</channel>
|
||||
</rss>
|
||||
@@ -0,0 +1,102 @@
|
||||
SHELL := /bin/bash
|
||||
FTPNCBI=ftp.ncbi.nlm.nih.gov
|
||||
GBURL=https://$(FTPNCBI)/genbank
|
||||
GBRELEASE_URL=$(GBURL)/GB_Release_Number
|
||||
|
||||
TAXOURL=https://$(FTPNCBI)/pub/taxonomy/taxdump.tar.gz
|
||||
|
||||
GBRELEASE:=$(shell curl $(GBRELEASE_URL))
|
||||
|
||||
GBDIV_ALL:=$(shell curl -L ${GBURL} \
|
||||
| grep -E 'gb.+\.seq\.gz' \
|
||||
| sed -E 's@^.*<a href="gb([^0-9]+)[0-9]+\.seq.gz.*$$@\1@' \
|
||||
| sort \
|
||||
| uniq)
|
||||
|
||||
GBDIV=bct inv mam phg pln pri rod vrl vrt
|
||||
DIRECTORIES=fasta fasta_fgs
|
||||
|
||||
GBFILE_ALL:=$(shell curl -L ${GBURL} \
|
||||
| grep -E "gb($$(tr ' ' '|' <<< "${GBDIV}"))[0-9]+" \
|
||||
| sed -E 's@^<a href="(gb.+.seq.gz)">.*$$@\1@')
|
||||
|
||||
|
||||
SUFFIXES += .d
|
||||
NODEPS:=clean taxonomy
|
||||
DEPFILES:=$(wildcard Release_$(GBRELEASE)/depends/*.d)
|
||||
|
||||
ifeq (0, $(words $(findstring $(MAKECMDGOALS), $(NODEPS))))
|
||||
#Chances are, these files don't exist. GMake will create them and
|
||||
#clean up automatically afterwards
|
||||
-include $(DEPFILES)
|
||||
endif
|
||||
|
||||
|
||||
all: depends directories FORCE
|
||||
@make downloads
|
||||
|
||||
downloads: taxonomy fasta_files
|
||||
@echo Genbank Release number $(GBRELEASE)
|
||||
@echo all divisions : $(GBDIV_ALL)
|
||||
|
||||
FORCE:
|
||||
|
||||
.PHONY: all directories depends taxonomy fasta_files FORCE
|
||||
|
||||
depends: directories Release_$(GBRELEASE)/depends/gbfiles.d Makefile
|
||||
|
||||
division: $(GBDIV)
|
||||
|
||||
taxonomy: directories Release_$(GBRELEASE)/taxonomy
|
||||
|
||||
directories: Release_$(GBRELEASE)/fasta Release_$(GBRELEASE)/stamp Release_$(GBRELEASE)/tmp
|
||||
|
||||
Release_$(GBRELEASE):
|
||||
@mkdir -p $@
|
||||
@echo Create $@ directory
|
||||
|
||||
Release_$(GBRELEASE)/fasta: Release_$(GBRELEASE)
|
||||
@mkdir -p $@
|
||||
@echo Create $@ directory
|
||||
|
||||
Release_$(GBRELEASE)/stamp: Release_$(GBRELEASE)
|
||||
@mkdir -p $@
|
||||
@echo Create $@ directory
|
||||
|
||||
Release_$(GBRELEASE)/tmp: Release_$(GBRELEASE)
|
||||
@mkdir -p $@
|
||||
@echo Create $@ directory
|
||||
|
||||
Release_$(GBRELEASE)/depends/gbfiles.d: Makefile
|
||||
@echo Create depends directory
|
||||
@mkdir -p Release_$(GBRELEASE)/depends
|
||||
@for f in ${GBFILE_ALL} ; do \
|
||||
echo -e "Release_$(GBRELEASE)/stamp/$$f.stamp:" ; \
|
||||
echo -e "\t@echo Downloading file : $$f..." ; \
|
||||
echo -e "\t@mkdir -p Release_$(GBRELEASE)/tmp" ; \
|
||||
echo -e "\t@mkdir -p Release_$(GBRELEASE)/stamp" ; \
|
||||
echo -e "\t@curl -L ${GBURL}/$$f > Release_$(GBRELEASE)/tmp/$$f && touch \$$@" ; \
|
||||
echo ; \
|
||||
div=$$(sed -E 's@^gb(...).*$$@\1@' <<< $$f) ; \
|
||||
fasta="Release_$(GBRELEASE)/fasta/$$div/$${f/.seq.gz/.fasta.gz}" ; \
|
||||
fasta_fgs="Release_$(GBRELEASE)/fasta_fgs/$$div/$${f/.seq.gz/.fasta.gz}" ; \
|
||||
fasta_files="$$fasta_files $$fasta" ; \
|
||||
fasta_fgs_files="$$fasta_fgs_files $$fasta_fgs" ; \
|
||||
echo -e "$$fasta: Release_$(GBRELEASE)/stamp/$$f.stamp" ; \
|
||||
echo -e "\t@echo converting file : \$$< in fasta" ; \
|
||||
echo -e "\t@mkdir -p Release_$(GBRELEASE)/fasta/$$div" ; \
|
||||
echo -e "\t@obiconvert -Z --fasta-output --skip-empty \\" ; \
|
||||
echo -e "\t Release_$(GBRELEASE)/tmp/$$f > Release_$(GBRELEASE)/tmp/$${f/.seq.gz/.fasta.gz} \\" ; \
|
||||
echo -e "\t && mv Release_$(GBRELEASE)/tmp/$${f/.seq.gz/.fasta.gz} \$$@ \\" ; \
|
||||
echo -e "\t && rm -f Release_$(GBRELEASE)/tmp/$$f \\" ; \
|
||||
echo -e "\t || rm -f \$$@" ; \
|
||||
echo -e "\t@echo conversion of $$@ done." ; \
|
||||
echo ; \
|
||||
done > $@ ; \
|
||||
echo >> $@ ; \
|
||||
echo "fasta_files: $$fasta_files" >> $@ ;
|
||||
|
||||
Release_$(GBRELEASE)/taxonomy:
|
||||
mkdir -p $@
|
||||
curl -iL $(TAXOURL) \
|
||||
| tar -C $@ -zxf -
|
||||
File diff suppressed because it is too large.
Load diff
@@ -0,0 +1,11 @@
|
||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||
<channel>
|
||||
<title>Prepare a local copy of Genbank on OBITools4 documentation</title>
|
||||
<link>http://metabar:8888/obidoc/docs/cookbook/local_genbank/</link>
|
||||
<description>Recent content in Prepare a local copy of Genbank on OBITools4 documentation</description>
|
||||
<generator>Hugo</generator>
|
||||
<language>en-us</language>
|
||||
<atom:link href="http://metabar:8888/obidoc/docs/cookbook/local_genbank/index.xml" rel="self" type="application/rss+xml" />
|
||||
</channel>
|
||||
</rss>
|
||||
File diff suppressed because it is too large.
Load diff
@@ -0,0 +1,12 @@
|
||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||
<channel>
|
||||
<title>Oxford Nanopore data analysis on OBITools4 documentation</title>
|
||||
<link>http://metabar:8888/obidoc/docs/cookbook/minion/</link>
|
||||
<description>Recent content in Oxford Nanopore data analysis on OBITools4 documentation</description>
|
||||
<generator>Hugo</generator>
|
||||
<language>en-us</language>
|
||||
<lastBuildDate></lastBuildDate>
|
||||
<atom:link href="http://metabar:8888/obidoc/docs/cookbook/minion/index.xml" rel="self" type="application/rss+xml" />
|
||||
</channel>
|
||||
</rss>
|
||||
File diff suppressed because it is too large.
Load diff
@@ -0,0 +1,12 @@
|
||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||
<channel>
|
||||
<title>Build a reference database on OBITools4 documentation</title>
|
||||
<link>http://metabar:8888/obidoc/docs/cookbook/reference_db/</link>
|
||||
<description>Recent content in Build a reference database on OBITools4 documentation</description>
|
||||
<generator>Hugo</generator>
|
||||
<language>en-us</language>
|
||||
<lastBuildDate></lastBuildDate>
|
||||
<atom:link href="http://metabar:8888/obidoc/docs/cookbook/reference_db/index.xml" rel="self" type="application/rss+xml" />
|
||||
</channel>
|
||||
</rss>
|
||||
File diff suppressed because it is too large.
Load diff
@@ -0,0 +1,11 @@
|
||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||
<channel>
|
||||
<title>File formats on OBITools4 documentation</title>
|
||||
<link>http://metabar:8888/obidoc/docs/file_format/</link>
|
||||
<description>Recent content in File formats on OBITools4 documentation</description>
|
||||
<generator>Hugo</generator>
|
||||
<language>en-us</language>
|
||||
<atom:link href="http://metabar:8888/obidoc/docs/file_format/index.xml" rel="self" type="application/rss+xml" />
|
||||
</channel>
|
||||
</rss>
|
||||
+1552
File diff suppressed because it is too large.
Load diff
@@ -0,0 +1,11 @@
|
||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
||||
<channel>
|
||||
<title>Annotation of sequences on OBITools4 documentation</title>
|
||||
<link>http://metabar:8888/obidoc/docs/file_format/sequence_files/annotations/</link>
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||||
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>AB061527 {"count":1,"definition":"Sorex unguiculatus mitochondrial NA, complete genome.","family_name":"Soricidae","family_taxid":9376,"genus_name":"Sorex","genus_taxid":9379,"obicleandb_level":"family","obicleandb_trusted":2.2137847111025621e-13,"species_name":"Sorex unguiculatus","species_taxid":62275,"taxid":62275}
|
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ttagccctaaacttaggtatttaatctaacaaaaatacccgtcagagaactactagcaat
|
||||
agcttaaaactcaaaggacttggcggtgctttatatccct
|
||||
>AL355887 {"count":2,"definition":"Human chromosome 14 NA sequence BAC R-179O11 of library RPCI-11 from chromosome 14 of Homo sapiens (Human)XXKW HTG.; HTGS_ACTIVFIN.","family_name":"Hominidae","family_taxid":9604,"genus_name":"Homo","genus_taxid":9605,"obicleandb_level":"genus","obicleandb_trusted":0,"species_name":"Homo sapiens","species_taxid":9606,"taxid":9606}
|
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|
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agcttaaaactcaaaggacctggcagttctttatatccct
|
||||
@@ -0,0 +1,8 @@
|
||||
@HELIUM_000100422_612GNAAXX:7:108:5640:3823#0/1 {"ali_dir":"left","ali_length":62,"mode":"alignment","pairing_mismatches":{"(T:26)->(G:13)":62,"(T:34)->(G:18)":48},"score":484,"score_norm":0.968,"seq_a_single":46,"seq_ab_match":60,"seq_b_single":46}
|
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CCCCCCCBCCCCCCCCCCCCCCCCCCCCCCBCCCCCBCCCCCCC<CcCccbe[`F`accXV<TA\RYU\\ee_e[XZ[XEEEEEEEEEE?EEEEEEEEEEDEEEEEEECCCCCCCCCCCCCCCCCCCCCCCACCCCCACCCCCCCCCCCCCCCC
|
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@HELIUM_000100422_612GNAAXX:7:97:14311:19299#0/1 {"ali_dir":"left","ali_length":62,"mode":"alignment","pairing_mismatches":{"(A:02)->(G:30)":104,"(A:34)->(G:14)":64,"(C:02)->(A:30)":86,"(C:02)->(T:20)":108,"(C:27)->(G:32)":83,"(C:34)->(G:18)":57,"(T:02)->(G:26)":87,"(T:22)->(G:14)":66,"(T:29)->(G:11)":62,"(T:32)->(G:30)":48},"score":283,"score_norm":0.839,"seq_a_single":46,"seq_ab_match":52,"seq_b_single":46}
|
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+30
@@ -0,0 +1,30 @@
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||||
taxid,parent,taxonomic_rank,scientific_name
|
||||
taxon:1 [root]@no rank,taxon:1 [root]@no rank,no rank,root
|
||||
taxon:131567 [cellular organisms]@no rank,taxon:1 [root]@no rank,no rank,cellular organisms
|
||||
taxon:2759 [Eukaryota]@superkingdom,taxon:131567 [cellular organisms]@no rank,superkingdom,Eukaryota
|
||||
taxon:33090 [Viridiplantae]@kingdom,taxon:2759 [Eukaryota]@superkingdom,kingdom,Viridiplantae
|
||||
taxon:35493 [Streptophyta]@phylum,taxon:33090 [Viridiplantae]@kingdom,phylum,Streptophyta
|
||||
taxon:131221 [Streptophytina]@subphylum,taxon:35493 [Streptophyta]@phylum,subphylum,Streptophytina
|
||||
taxon:3193 [Embryophyta]@clade,taxon:131221 [Streptophytina]@subphylum,clade,Embryophyta
|
||||
taxon:58023 [Tracheophyta]@clade,taxon:3193 [Embryophyta]@clade,clade,Tracheophyta
|
||||
taxon:78536 [Euphyllophyta]@clade,taxon:58023 [Tracheophyta]@clade,clade,Euphyllophyta
|
||||
taxon:58024 [Spermatophyta]@clade,taxon:78536 [Euphyllophyta]@clade,clade,Spermatophyta
|
||||
taxon:3398 [Magnoliopsida]@class,taxon:58024 [Spermatophyta]@clade,class,Magnoliopsida
|
||||
taxon:1437183 [Mesangiospermae]@clade,taxon:3398 [Magnoliopsida]@class,clade,Mesangiospermae
|
||||
taxon:71240 [eudicotyledons]@clade,taxon:1437183 [Mesangiospermae]@clade,clade,eudicotyledons
|
||||
taxon:91827 [Gunneridae]@clade,taxon:71240 [eudicotyledons]@clade,clade,Gunneridae
|
||||
taxon:1437201 [Pentapetalae]@clade,taxon:91827 [Gunneridae]@clade,clade,Pentapetalae
|
||||
taxon:71275 [rosids]@clade,taxon:1437201 [Pentapetalae]@clade,clade,rosids
|
||||
taxon:91835 [fabids]@clade,taxon:71275 [rosids]@clade,clade,fabids
|
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taxon:3502 [Fagales]@order,taxon:91835 [fabids]@clade,order,Fagales
|
||||
taxon:3514 [Betulaceae]@family,taxon:3502 [Fagales]@order,family,Betulaceae
|
||||
taxon:3504 [Betula]@genus,taxon:3514 [Betulaceae]@family,genus,Betula
|
||||
taxon:1685988 [Betula murrayana]@species,taxon:3504 [Betula]@genus,species,Betula murrayana
|
||||
taxon:361422 [Betula ovalifolia]@species,taxon:3504 [Betula]@genus,species,Betula ovalifolia
|
||||
taxon:1685972 [Betula x caerulea]@species,taxon:3504 [Betula]@genus,species,Betula x caerulea
|
||||
taxon:216986 [Betula schmidtii]@species,taxon:3504 [Betula]@genus,species,Betula schmidtii
|
||||
taxon:312791 [Betula michauxii]@species,taxon:3504 [Betula]@genus,species,Betula michauxii
|
||||
taxon:3015411 [Betula pamirica]@species,taxon:3504 [Betula]@genus,species,Betula pamirica
|
||||
taxon:312792 [Betula raddeana]@species,taxon:3504 [Betula]@genus,species,Betula raddeana
|
||||
taxon:216991 [Betula humilis]@species,taxon:3504 [Betula]@genus,species,Betula humilis
|
||||
taxon:2218489 [Betula ovalifolia x Betula ermanii]@species,taxon:3504 [Betula]@genus,species,Betula ovalifolia x Betula ermanii
|
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<description><h2 id="what-are-obitools4">
 What are OBITools4?
 <a class="anchor" href="#what-are-obitools4">#</a>
</h2>
<p>The development of <abbr title="A set of unix command line tools for manipulating DNA metabarcoding data">OBITools</abbr>
 began at 
 <a href="https://leca.osug.fr"><abbr title="LECA: Laboratoire d&#39;écologie Alpine - Laboratory for Alpine Ecology">LECA</abbr>
 
 </a> (
 <a href="https://www.univ-grenoble-alpes.fr/">University of Grenoble</a>) in the early 2000s, at the same time as the development of DNA metabarcoding methods in the same laboratory. The idea behind the OBITools project was to provide a set of UNIX command-line tools that mimic standard UNIX shell commands such as <code>grep</code>, <code>uniq</code> or <code>wc</code>, but which work on DNA sequence files. Unlike standard UNIX tools, where the processing unit is a line of text, with OBITools the processing unit is a sequence record. In addition, some commands implementing algorithms specific to the processing of DNA metabarcoding data have been added, making <abbr title="A set of unix command line tools for manipulating DNA metabarcoding data">OBITools</abbr>
 one of the sequence processing tools widely used on UNIX-like systems, suitable for the analysis of DNA metabarcoding data.</p></description>
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<title>Patterns on OBITools4 documentation</title>
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<title>Regular Expressions</title>
|
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<guid>http://metabar:8888/obidoc/docs/patterns/regular/</guid>
|
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<description><h1 id="regular-expressions">
 Regular Expressions
 <a class="anchor" href="#regular-expressions">#</a>
</h1>
<p>Regular expressions are a powerful tool for describing patterns in text. They are used in several <abbr title="A set of unix command line tools for manipulating DNA metabarcoding data">OBITools</abbr>
 like <a href="http://metabar:8888/obidoc/obitools/obigrep/">
 <abbr title="obigrep: filter a sequence file"><code>obigrep</code></abbr>
 </a>, <a href="http://metabar:8888/obidoc/obitools/obiannotate/">
 <abbr title="obiannotate: edit sequence annotations"><code>obiannotate</code></abbr>
 </a> or <a href="http://metabar:8888/obidoc/obitools/obiscript/">
 <abbr title="obiscript: apply a LUA script to a sequence file"><code>obiscript</code></abbr>
 </a>.</p>
<h2 id="single-characters">
 Single characters
 <a class="anchor" href="#single-characters">#</a>
</h2>
<table>
 <thead>
 <tr>
 <th>Pattern</th>
 <th>Description</th>
 </tr>
 </thead>
 <tbody>
 <tr>
 <td><code>.</code></td>
 <td>any character, possibly including newline (flag s=true)</td>
 </tr>
 <tr>
 <td><code>[xyz]</code></td>
 <td>character class</td>
 </tr>
 <tr>
 <td><code>[^xyz]</code></td>
 <td>negated character class</td>
 </tr>
 <tr>
 <td><code>[[:alpha:]]</code></td>
 <td>ASCII character class</td>
 </tr>
 <tr>
 <td><code>[[:^alpha:]]</code></td>
 <td>negated ASCII character class</td>
 </tr>
 </tbody>
</table>
<h2 id="composites">
 Composites
 <a class="anchor" href="#composites">#</a>
</h2>
<table>
 <thead>
 <tr>
 <th>Pattern</th>
 <th>Description</th>
 </tr>
 </thead>
 <tbody>
 <tr>
 <td><code>xy</code></td>
 <td>x followed by y</td>
 </tr>
 <tr>
 <td><code>x|y</code></td>
 <td>x or y (prefer x)</td>
 </tr>
 </tbody>
</table>
<h2 id="repetitions">
 Repetitions
 <a class="anchor" href="#repetitions">#</a>
</h2>
<table>
 <thead>
 <tr>
 <th>Pattern</th>
 <th>Description</th>
 </tr>
 </thead>
 <tbody>
 <tr>
 <td><code>x*</code></td>
 <td>zero or more x, prefer more</td>
 </tr>
 <tr>
 <td><code>x+</code></td>
 <td>one or more x, prefer more</td>
 </tr>
 <tr>
 <td><code>x?</code></td>
 <td>zero or one x, prefer one</td>
 </tr>
 <tr>
 <td><code>x{n,m}</code></td>
 <td>n or n+1 or &hellip; or m x, prefer more</td>
 </tr>
 <tr>
 <td><code>x{n,}</code></td>
 <td>n or more x, prefer more</td>
 </tr>
 <tr>
 <td><code>x{n}</code></td>
 <td>exactly n x</td>
 </tr>
 <tr>
 <td><code>x*?</code></td>
 <td>zero or more x, prefer fewer</td>
 </tr>
 <tr>
 <td><code>x+?</code></td>
 <td>one or more x, prefer fewer</td>
 </tr>
 <tr>
 <td><code>x??</code></td>
 <td>zero or one x, prefer zero</td>
 Line truncated
|
||||
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|
||||
<item>
|
||||
<title>DNA Patterns</title>
|
||||
<link>http://metabar:8888/obidoc/docs/patterns/dnagrep/</link>
|
||||
<pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
|
||||
<guid>http://metabar:8888/obidoc/docs/patterns/dnagrep/</guid>
|
||||
<description><h1 id="dna-patterns">
 DNA Patterns
 <a class="anchor" href="#dna-patterns">#</a>
</h1>
<p>DNA patterns are useful for describing short DNA sequences like oligonucleotides. They are used by several <abbr title="A set of unix command line tools for manipulating DNA metabarcoding data">OBITools</abbr>
 like <a href="http://metabar:8888/obidoc/obitools/obimultiplex/">
 <abbr title="obimultiplex: "><code>obimultiplex</code></abbr>
 </a>, <a href="http://metabar:8888/obidoc/obitools/obipcr/">
 <abbr title="obipcr: the electronic PCR tool"><code>obipcr</code></abbr>
 </a> or <a href="http://metabar:8888/obidoc/obitools/obigrep/">
 <abbr title="obigrep: filter a sequence file"><code>obigrep</code></abbr>
 </a>. The advantage of using DNA patterns over classical regular expressions is that they can be matched with errors. Allowed errors can be simple mismatches, or mismatches and insertions/deletions.</p></description>
|
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|
||||
@M01334:147:000000000-LBRVD:1:1101:14968:1570 1:N:0:CTCACCAA+CTAGGCAA
|
||||
TGTTCCACGGGCAATCCTGAGCCAAATCTTTCATTTTGAAAAAATGAGAGATATAATGTATCTCTTATTTATTATAAGAAATAAAATATTTCTTATCTAATATTAAAGTTAGGTGCAGAGACTCAATGGGTGGAACTAGATCGGATGTGCA
|
||||
+
|
||||
11>A>@3@A11>ACFFEG110BFB00BAFGHE2DFGG201110/B11111/D1D2222D2FDFDFGDGHHBGG2F222110D11@1D1FGHFHGFF@GE1F2FG22112B220F1@111/0>BF11B210B>//11B1<1BB<///<1122
|
||||
@M01334:147:000000000-LBRVD:1:1101:15946:1586 1:N:0:CTCACCAA+CTAGGCAA
|
||||
TCCTAACCCCATTGAGTCTCTGCACCTATCTTTAATATTAGATAAGAAATATTTTATTTCTTATAATAAATAAGAGATATTTTATATCTCTCATTTTTTCAAAATGAAAGATTTGGCTCAGGATTGCCCACGTAACGGAGATCGGAAGAGC
|
||||
+
|
||||
1>>A111>>>AFGGB1FFGFGFF3BBF1GGHHH33D2GH2B1D211110D1DGHHBFGGGGG2FA2F221F21A1F0D1DGHH2FAFFGFHFFGHHHHGG22@1BD111@0FFHE11GC1001BGF1B1B/EF00??////BF////<000
|
||||
@M01334:147:000000000-LBRVD:1:1101:15399:1590 1:N:0:CTCACCAA+CTAGGCAA
|
||||
TGTTCCACCCATTGAGTCTCTGCACCTATCTTTAATATTAGATAAGAAATATTTTACTTCTTATAATAAATAAGAGTTATTTTATATCTCTCATTTTTTCAAAATGAAAGATTTGGCTCAGGATTGCCCGTGGAACTAGATCGGAAGAGCA
|
||||
+
|
||||
11>A>@3B>>1CF111BBFAG3A3AAF1FFGHHF3FBGH221F211110D1DGHH2BBGBFF2F22D221D211111A2DDGG2F2FFFEGD1FFHHHGFD221B111110BFGD11F@1001BF0@@1/EA//1>F1B1FD/////00<1
|
||||
@M01334:147:000000000-LBRVD:1:1101:13773:1687 1:N:0:CTCACCAA+CTAGGCAA
|
||||
CTCGGATCACCATTGAGTCTCTGCACCTATCTTTAATATTAGATAAGAAAAAATATTATTTCTTATCTGAAATAAGAAATATTTTATATATTTCTTTTTCTCAAAATGAAAGATTTGGCTCAGGATTGCCCTGATCCGAGGGATAGCACCA
|
||||
+
|
||||
3AAAAAADFFFFGGGGFGGGGGHHHHHHFHHHHHHHHGHHHHGHGGHFFHHHCGFHHHHHHHHHHHHHGHHGGFHFFHHHGHHHHBHHHGHHHHHHHHHHHHHFFHHFBDFBCGHHF4BGHFGFFHHBDGFHHEHHFAAEECEGF3FDGFC
|
||||
@@ -0,0 +1,12 @@
|
||||
>AY189646 {"count":1,"definition":"Homo sapiens clone arCan119 12S ribosomal RNA gene, partial sequence; mitochondrial gene for mitochondrial product.","species_name":"Homo sapiens","taxid":"taxon:9606 [Homo sapiens]@species"}
|
||||
ttagccctaaacctcaacagttaaatcaacaaaactgctcgccagaacactacgrgccac
|
||||
agcttaaaactcaaaggacctggcggtgcttcatatccct
|
||||
>AF023201 {"count":1,"definition":"Snyderichthys copei 12S ribosomal RNA gene, mitochondrial gene for mitochondrial RNA, complete sequence.","species_name":"Snyderichthys copei","taxid":"67561"}
|
||||
tcagccataaacctagatgtccagctacagttagacatccgcccgggtactacgagcatt
|
||||
agcttgaaacccaaaggacctgacggtgccttagaccccc
|
||||
>JN897380 {"count":1,"definition":"Nihonotrypaea thermophila mitochondrion, complete genome.","species_name":"Nihonotrypaea thermophila","taxid":"1114968"}
|
||||
tagccttaacaaacatactaaaatattaaaagttatggtctctaaatttaaaggatttgg
|
||||
cggtaatttagtccag
|
||||
>KC236422 {"count":1,"definition":"Nihonotrypaea japonica mitochondrion, complete genome.","species_name":"Nihonotrypaea japonica","taxid":"5799994"}
|
||||
cagctttaacaaacatactaaaatattaaaagttatggtctctaaatttaaaggatttgg
|
||||
cggtaatttagtccag
|
||||
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