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Eric Coissac
2025-11-16 14:56:03 +01:00
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.gitignore vendored
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/web_src/**/*_files /web_src/**/*_files
/web_src/**/*_cache /web_src/**/*_cache
/.luarc.json /.luarc.json
*.log /sandbox
*.log

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jupyterhub_volumes/course/unix.ipynb
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{
"cells": [
{
"cell_type": "markdown",
"id": "30438c30",
"metadata": {},
"source": [
"# Unix Essentials — Bash Practice Notebook\n",
"\n",
"This notebook contains 50 small Bash exercises grouped by topic.\n",
"Each exercise includes a hidden solution that can be revealed in Jupyter."
]
},
{
"cell_type": "markdown",
"id": "39d711f9",
"metadata": {},
"source": [
"## Series 1 — Paths and Directories"
]
},
{
"cell_type": "markdown",
"id": "6fb7335e",
"metadata": {},
"source": [
"### Exercise 1.1 — Show your current working directory"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "2b8575f3",
"metadata": {},
"outputs": [],
"source": [
"# your work here\n",
"pwd"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "21f63bb0",
"metadata": {
"jupyter": {
"outputs_hidden": true,
"source_hidden": true
}
},
"outputs": [],
"source": [
"# Solution\n",
"pwd"
]
},
{
"cell_type": "markdown",
"id": "61a624bf",
"metadata": {},
"source": [
"### Exercise 1.2 — Create a new directory named `testdir`"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "4a4df387",
"metadata": {},
"outputs": [],
"source": [
"# your work here\n",
"mkdir testdir"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "2b5cfbca",
"metadata": {
"jupyter": {
"outputs_hidden": true,
"source_hidden": true
}
},
"outputs": [],
"source": [
"# Solution\n",
"mkdir testdir"
]
},
{
"cell_type": "markdown",
"id": "2dccbb61",
"metadata": {},
"source": [
"### Exercise 1.3 — Move into `testdir` using a relative path"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "fb73ca3c",
"metadata": {},
"outputs": [],
"source": [
"# your work here\n",
"cd testdir"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "ba670a20",
"metadata": {
"jupyter": {
"outputs_hidden": true,
"source_hidden": true
}
},
"outputs": [],
"source": [
"# Solution\n",
"cd testdir"
]
},
{
"cell_type": "markdown",
"id": "4f7e5817",
"metadata": {},
"source": [
"### Exercise 1.4 — Create two subdirectories `a` and `b` in one command"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "30be8f44",
"metadata": {},
"outputs": [],
"source": [
"# your work here\n",
"mkdir a b"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "caf92714",
"metadata": {
"jupyter": {
"outputs_hidden": true,
"source_hidden": true
}
},
"outputs": [],
"source": [
"# Solution\n",
"mkdir a b"
]
},
{
"cell_type": "markdown",
"id": "edec9041",
"metadata": {},
"source": [
"### Exercise 1.5 — Return to the parent directory using `..`"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "32a0f1df",
"metadata": {},
"outputs": [],
"source": [
"# your work here\n",
"cd .."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "2a0aa92f",
"metadata": {
"jupyter": {
"outputs_hidden": true,
"source_hidden": true
}
},
"outputs": [],
"source": [
"# Solution\n",
"cd .."
]
},
{
"cell_type": "markdown",
"id": "31917159",
"metadata": {},
"source": [
"### Exercise 1.6 — Create nested directories `one/two/three` in a single command"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "c0a313c3",
"metadata": {},
"outputs": [],
"source": [
"# your work here\n",
"mkdir -p one/two/three"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "4af63dce",
"metadata": {
"jupyter": {
"outputs_hidden": true,
"source_hidden": true
}
},
"outputs": [],
"source": [
"# Solution\n",
"mkdir -p one/two/three"
]
},
{
"cell_type": "markdown",
"id": "24ee949e",
"metadata": {},
"source": [
"### Exercise 1.7 — List the absolute path of the current directory"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "8258fff7",
"metadata": {},
"outputs": [],
"source": [
"# your work here\n",
"pwd"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "a6a062b2",
"metadata": {
"jupyter": {
"outputs_hidden": true,
"source_hidden": true
}
},
"outputs": [],
"source": [
"# Solution\n",
"pwd"
]
},
{
"cell_type": "markdown",
"id": "6d724d3e",
"metadata": {},
"source": [
"### Exercise 1.8 — Create a directory using an absolute path"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "5f497f7c",
"metadata": {},
"outputs": [],
"source": [
"# your work here\n",
"mkdir /tmp/mydir"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "1d1d4e27",
"metadata": {
"jupyter": {
"outputs_hidden": true,
"source_hidden": true
}
},
"outputs": [],
"source": [
"# Solution\n",
"mkdir /tmp/mydir"
]
},
{
"cell_type": "markdown",
"id": "0a4cbe5b",
"metadata": {},
"source": [
"### Exercise 1.9 — Display both `.` and `..` directories with `ls -a`"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "7d962a9f",
"metadata": {},
"outputs": [],
"source": [
"# your work here\n",
"ls -a"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "91994de2",
"metadata": {
"jupyter": {
"outputs_hidden": true,
"source_hidden": true
}
},
"outputs": [],
"source": [
"# Solution\n",
"ls -a"
]
},
{
"cell_type": "markdown",
"id": "e147ff34",
"metadata": {},
"source": [
"### Exercise 1.10 — Remove the directory `/tmp/mydir`"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "dcae28e3",
"metadata": {},
"outputs": [],
"source": [
"# your work here\n",
"rmdir /tmp/mydir"
]
},
{
"cell_type": "code",
"execution_count": null,
"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"
]
},
{
"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
}

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---
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<75>rieur <20> 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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>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

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#!/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'])

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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} \$$@ \\" ; \
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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 -

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ttagccctaaacacaagtaattaatataacaaaattatgcgccagagtactgccggcaat
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ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
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ttagccctaaacacaaataattatataaacaaaattattcgccagagtactaccggcaac
agcccaaaactcaaaggacttggcggtgctttataccctt
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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
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>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

24
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>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

9
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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
1 id count obitag_bestid obitag_bestmatch obitag_match_count obitag_rank obitag_similarity_method seq_number taxid sequence
2 seq0001 10172 0.9797979797979798 AY227529 1 genus lcs 1 taxon:9992 [Marmota]@genus ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaacagcctgaaactcaaaggacttggcggtgctttacatccct
3 seq0002 260 0.9405940594059405 AF154263 9 infraorder lcs 2 taxon:35500 [Pecora]@infraorder ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaacagcttaaaactcaaaggacttggcggtgctttataccctt
4 seq0003 7146 1 AB245427 1 species lcs 3 taxon:9860 [Cervus elaphus]@species ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
5 seq0004 87 0.9494949494949495 AY227530 2 tribe lcs 4 taxon:337730 [Marmotini]@tribe ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaatagcttaaaactcaaaggacttggcggtgctttatatccct
6 seq0005 95 0.9595959595959596 AC187326 1 subspecies lcs 5 taxon:9615 [Canis lupus familiaris]@subspecies ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaacagattaaacctcaaaggacttggcagtgctttatacccct
7 seq0006 12004 1 AJ885202 1 species lcs 6 taxon:9858 [Capreolus capreolus]@species ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
8 seq0007 319 1 AJ972683 1 species lcs 7 taxon:9858 [Capreolus capreolus]@species ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
9 seq0008 366 1 AB048590 1 genus lcs 8 taxon:9611 [Canis]@genus ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaatagcttaaaactcaaaggacttggcggtgctttatatccct

6
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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
1 id seq0001 seq0002 seq0003 seq0004 seq0005 seq0006 seq0007 seq0008
2 29a_F260619 0 337 0 0 105 5789 376 1
3 15a_F730814 0 0 0 0 0 8822 0 5
4 13a_F730603 0 0 8039 0 0 0 0 17
5 26a_F040644 12205 0 0 202 12 0 0 468

24
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>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

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@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
1 @param,matching,strict
2 @param,primer_mismatches,2
3 @param,indels,false
4 experiment,sample,sample_tag,forward_primer,reverse_primer
5 wolf_diet,13a_F730603,aattaac,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
6 wolf_diet,15a_F730814,gaagtag,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
7 wolf_diet,26a_F040644,gaatatc,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
8 wolf_diet,29a_F260619,gcctcct,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG

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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 -

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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}
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

8
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@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}
ccgcctcctttagataccccactatgcttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttatacccttctagaggagcctgttctaaggaggcgg
+
CCCCCCCBCCCCCCCCCCCCCCCCCCCCCCBCCCCCBCCCCCCC<CcCccbe[`F`accXV<TA\RYU\\ee_e[XZ[XEEEEEEEEEE?EEEEEEEEEEDEEEEEEECCCCCCCCCCCCCCCCCCCCCCCACCCCCACCCCCCCCCCCCCCCC
@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}
ccgcctcctttagataccccactatgcttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaagagcttaaaactcaaaggacttggcggtgctttatacccttctagaggagcctgttctaaggaggcgg
+
CCCCCCCCCCCCCCCCCCCCCCCBBCCC?BCCCCCBC?CCCC@@;AVA`cWeb_TYC\UIN?IDP8QJMKRPVGLQAFPPc`AbAFB5A4>AAA56A><>8>>F@A><8??@BB+<?;?C@9CCCCCC<CC=CCCCCCCCCBC?CBCCCCC@CC

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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
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
1 taxid parent taxonomic_rank scientific_name
2 taxon:1 [root]@no rank taxon:1 [root]@no rank no rank root
3 taxon:131567 [cellular organisms]@no rank taxon:1 [root]@no rank no rank cellular organisms
4 taxon:2759 [Eukaryota]@superkingdom taxon:131567 [cellular organisms]@no rank superkingdom Eukaryota
5 taxon:33090 [Viridiplantae]@kingdom taxon:2759 [Eukaryota]@superkingdom kingdom Viridiplantae
6 taxon:35493 [Streptophyta]@phylum taxon:33090 [Viridiplantae]@kingdom phylum Streptophyta
7 taxon:131221 [Streptophytina]@subphylum taxon:35493 [Streptophyta]@phylum subphylum Streptophytina
8 taxon:3193 [Embryophyta]@clade taxon:131221 [Streptophytina]@subphylum clade Embryophyta
9 taxon:58023 [Tracheophyta]@clade taxon:3193 [Embryophyta]@clade clade Tracheophyta
10 taxon:78536 [Euphyllophyta]@clade taxon:58023 [Tracheophyta]@clade clade Euphyllophyta
11 taxon:58024 [Spermatophyta]@clade taxon:78536 [Euphyllophyta]@clade clade Spermatophyta
12 taxon:3398 [Magnoliopsida]@class taxon:58024 [Spermatophyta]@clade class Magnoliopsida
13 taxon:1437183 [Mesangiospermae]@clade taxon:3398 [Magnoliopsida]@class clade Mesangiospermae
14 taxon:71240 [eudicotyledons]@clade taxon:1437183 [Mesangiospermae]@clade clade eudicotyledons
15 taxon:91827 [Gunneridae]@clade taxon:71240 [eudicotyledons]@clade clade Gunneridae
16 taxon:1437201 [Pentapetalae]@clade taxon:91827 [Gunneridae]@clade clade Pentapetalae
17 taxon:71275 [rosids]@clade taxon:1437201 [Pentapetalae]@clade clade rosids
18 taxon:91835 [fabids]@clade taxon:71275 [rosids]@clade clade fabids
19 taxon:3502 [Fagales]@order taxon:91835 [fabids]@clade order Fagales
20 taxon:3514 [Betulaceae]@family taxon:3502 [Fagales]@order family Betulaceae
21 taxon:3504 [Betula]@genus taxon:3514 [Betulaceae]@family genus Betula
22 taxon:1685988 [Betula murrayana]@species taxon:3504 [Betula]@genus species Betula murrayana
23 taxon:361422 [Betula ovalifolia]@species taxon:3504 [Betula]@genus species Betula ovalifolia
24 taxon:1685972 [Betula x caerulea]@species taxon:3504 [Betula]@genus species Betula x caerulea
25 taxon:216986 [Betula schmidtii]@species taxon:3504 [Betula]@genus species Betula schmidtii
26 taxon:312791 [Betula michauxii]@species taxon:3504 [Betula]@genus species Betula michauxii
27 taxon:3015411 [Betula pamirica]@species taxon:3504 [Betula]@genus species Betula pamirica
28 taxon:312792 [Betula raddeana]@species taxon:3504 [Betula]@genus species Betula raddeana
29 taxon:216991 [Betula humilis]@species taxon:3504 [Betula]@genus species Betula humilis
30 taxon:2218489 [Betula ovalifolia x Betula ermanii]@species taxon:3504 [Betula]@genus species Betula ovalifolia x Betula ermanii

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@M01334:147:000000000-LBRVD:1:1101:14968:1570 1:N:0:CTCACCAA+CTAGGCAA
TGTTCCACGGGCAATCCTGAGCCAAATCTTTCATTTTGAAAAAATGAGAGATATAATGTATCTCTTATTTATTATAAGAAATAAAATATTTCTTATCTAATATTAAAGTTAGGTGCAGAGACTCAATGGGTGGAACTAGATCGGATGTGCA
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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
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1>>A111>>>AFGGB1FFGFGFF3BBF1GGHHH33D2GH2B1D211110D1DGHHBFGGGGG2FA2F221F21A1F0D1DGHH2FAFFGFHFFGHHHHGG22@1BD111@0FFHE11GC1001BGF1B1B/EF00??////BF////<000
@M01334:147:000000000-LBRVD:1:1101:15399:1590 1:N:0:CTCACCAA+CTAGGCAA
TGTTCCACCCATTGAGTCTCTGCACCTATCTTTAATATTAGATAAGAAATATTTTACTTCTTATAATAAATAAGAGTTATTTTATATCTCTCATTTTTTCAAAATGAAAGATTTGGCTCAGGATTGCCCGTGGAACTAGATCGGAAGAGCA
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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
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3AAAAAADFFFFGGGGFGGGGGHHHHHHFHHHHHHHHGHHHHGHGGHFFHHHCGFHHHHHHHHHHHHHGHHGGFHFFHHHGHHHHBHHHGHHHHHHHHHHHHHFFHHFBDFBCGHHF4BGHFGFFHHBDGFHHEHHFAAEECEGF3FDGFC

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>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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