CDS detector added
Former-commit-id: a72f30f90d22cc3c7ff6059e0254e47911bb5af1 Former-commit-id: db0264bdbe5136b6e6dc44e4788175a257439643
This commit is contained in:
alain viari
13
README.txt
13
README.txt
@ -10,22 +10,27 @@
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#
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# First check if binaries have been already compiled for your port
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#
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# $ scripts/check_port
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# $ scripts/check_port.sh
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#
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# if it prints :
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#
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# + port <PORTNAME> is correctly installed
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# + checking port compilation OK
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#
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# then everything is fine
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#
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# if it prints :
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#
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# ! port <PORTNAME> not installed
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# ! Please read README.txt for proper installation
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# + port not yet compiled
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#
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# then, you should first compile binaries for your port
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# please consult: src/README.txt for details
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#
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# if it prints smthing like
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# * XXX version A.B.C (should be >= X.Y.Z)
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# * please consider installing XXX from src/_unix_tools_
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#
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# then, you should first compile some unix tools binaries for your port
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# please consult: src/README.txt for details
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#
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# -------------------------
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# -2- Distribution organisation
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@ -19,8 +19,8 @@
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# -- CAUTION -- Works as long than the script
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# is not called through a symlink
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SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})"
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source ${SCRIPT_DIR}/../../normalize/lib/lookforIR.lib.sh
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THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
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source ${THIS_DIR}/../../normalize/lib/lookforIR.lib.sh
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pushTmpDir ORG.ir
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@ -24,8 +24,8 @@
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# -- CAUTION -- Works as long than the script
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# is not called through a symlink
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SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})"
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source ${SCRIPT_DIR}/../lib/lookforIR.lib.sh
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THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
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source ${THIS_DIR}/../lib/lookforIR.lib.sh
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ORG_DEBUG=1
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@ -1,4 +1,4 @@
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source "${SCRIPT_DIR}/../../../scripts/bash_init.sh"
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source "${THIS_DIR}/../../../scripts/bash_init.sh"
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SELECTIR="${PROG_DIR}/../../normalize/lib/selectIR.py"
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@ -6,8 +6,8 @@
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# -- CAUTION -- Works as long than the script
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# is not called through a symlink
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SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${SCRIPT_DIR}/../../../scripts/bash_init.sh"
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THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${THIS_DIR}/../../../scripts/bash_init.sh"
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pushTmpDir ORG.buildSCDB
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@ -23,8 +23,8 @@
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# -- CAUTION -- Works as long than the script
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# is not called through a symlink
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SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${SCRIPT_DIR}/../../../scripts/bash_init.sh"
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THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${THIS_DIR}/../../../scripts/bash_init.sh"
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pushTmpDir ORG.coorienteSC
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@ -16,8 +16,8 @@
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# -- CAUTION -- Works as long than the script
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# is not called through a symlink
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SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${SCRIPT_DIR}/../../../scripts/bash_init.sh"
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THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${THIS_DIR}/../../../scripts/bash_init.sh"
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pushTmpDir ORG.rrna
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@ -6,8 +6,8 @@
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# -- CAUTION -- Works as long than the script
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# is not called through a symlink
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SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${SCRIPT_DIR}/../../../scripts/bash_init.sh"
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THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${THIS_DIR}/../../../scripts/bash_init.sh"
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function fasta1li {
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@ -6,8 +6,8 @@
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# -- CAUTION -- Works as long than the script
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# is not called through a symlink
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SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${SCRIPT_DIR}/../../../scripts/bash_init.sh"
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THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${THIS_DIR}/../../../scripts/bash_init.sh"
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function revcomp {
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@ -5,7 +5,7 @@
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#========================================================================================
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#
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# Annotate tRNA based on the Aragorn software predictions.
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#
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# go_trna.sh <FASTAFILE>
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#
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# - <FASTAFILE> : The fasta file containing the genome to annotate
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@ -14,10 +14,10 @@
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#
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#========================================================================================
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# -- CAUTION -- Works as long than the script
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# -- CAUTION -- Works as long as the script
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# is not called through a symlink
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SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${SCRIPT_DIR}/../../../scripts/bash_init.sh"
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THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${THIS_DIR}/../../../scripts/bash_init.sh"
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pushTmpDir ORG.trna
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@ -6,8 +6,8 @@
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# -- CAUTION -- Works as long than the script
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# is not called through a symlink
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SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${SCRIPT_DIR}/../../../scripts/bash_init.sh"
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THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${THIS_DIR}/../../../scripts/bash_init.sh"
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function fasta1li {
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@ -6,8 +6,8 @@
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# -- CAUTION -- Works as long than the script
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# is not called through a symlink
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SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${SCRIPT_DIR}/../../../scripts/bash_init.sh"
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THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${THIS_DIR}/../../../scripts/bash_init.sh"
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function taxid {
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egrep '/db_xref="taxon:[0-9]+"' $1 | \
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@ -1,26 +1,18 @@
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#!/bin/bash
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#
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#
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#
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# Annotate tRNA
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# Annotate Organelle
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#
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#========================================================================================
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#
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# Annotate tRNA based on the Aragorn software predictions.
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# go_trna.sh <FASTAFILE>
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#
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# - <FASTAFILE> : The fasta file containing the genome to annotate
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#
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# Results are printed to the standart output
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#
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#========================================================================================
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# -- CAUTION -- Works as long than the script
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# -- CAUTION -- Works as long as the script
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# is not called through a symlink
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SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${SCRIPT_DIR}/scripts/bash_init.sh"
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THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${THIS_DIR}/scripts/bash_init.sh"
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pushTmpDir ORG.organnot
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@ -52,7 +44,10 @@ pushTmpDir ORG.organnot
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loginfo "Annotating the rRNA genes..."
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${PROG_DIR}/detectors/rrna/bin/go_rrna.sh ${QUERY} >> "${RESULTS}.annot"
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loginfo "Done."
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loginfo "Annotating the CDS..."
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${PROG_DIR}/detectors/cds/bin/go_cds.sh ${QUERY} >> "${RESULTS}.annot"
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loginfo "Done."
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loginfo "Printing annotations header..."
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echo "XX"
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@ -143,27 +143,35 @@ function formatfasta {
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#
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#
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# The absolute path to the ORG.Annote home direcotory
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# The absolute path to the ORG.Annot home directory
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ORG_HOME=`getAbsolutePath $(dirname ${BASH_SOURCE[0]})/..`
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ORG_PORTNAME=`${ORG_HOME}/config/guess_port` # The architecture running the ORG.Annnote instance
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ORG_PORTNAME=`${ORG_HOME}/config/guess_port` # The architecture running the ORG.Annot instance
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BIN_DIR="${ORG_HOME}/ports/${ORG_PORTNAME}/bin" # Directory containing binaries for this port
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SCRIPT_DIR="${ORG_HOME}/scripts" # Directory containing scripts utilities
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PROG_DIR="$(getAbsolutePath $(dirname $0))" # Directory containing the main script file
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DATA_DIR="${ORG_HOME}/data" # Directory containing reference data for the annotation
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LIB_DIR="$(getAbsolutePath ${PROG_DIR}/../lib)" # Directory containing the main script libraries
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CALL_DIR="$(getAbsolutePath $(pwd))" # Directory from where the main script is called
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IR_DATA_DIR="${DATA_DIR}/ir" # Directory containing data related to the
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# Inverted repeat strucuture
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DATA_DIR="${ORG_HOME}/data" # Directory containing reference data for the annotation
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IR_DATA_DIR="${DATA_DIR}/ir" # Directory containing data related to
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# IRs detection
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TRNA_DATA_DIR="${DATA_DIR}/trna" # Directory containing data related to
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# tRNAs detection
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CDS_DATA_DIR="${DATA_DIR}/trna" # Directory containing data related to
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# CDSs detection
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TRNA_DATA_DIR="${DATA_DIR}/trna" # Directory containing data related to the
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# tRNA detection
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RRNA_DATA_DIR="${DATA_DIR}/rrna" # Directory containing data related to the
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# rRNA dectection
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RRNA_DATA_DIR="${DATA_DIR}/rrna" # Directory containing data related to
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# rRNAs detection
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#
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@ -179,11 +187,10 @@ RRNA_DATA_DIR="${DATA_DIR}/rrna" # Directory containing data related to the
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#
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# We alter the path to include the bin dir corresponding to the port
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PATH="${ORG_HOME}/ports/${ORG_PORTNAME}/bin:${PATH}"
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PATH="${SCRIPT_DIR}:${BIN_DIR}:${PATH}"
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export PATH
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# Force to basic international setting for a correction behaviour of AWK on mac with float
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export LANG=C
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export LC_ALL=C
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@ -1,20 +0,0 @@
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#!/bin/csh
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#
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# check if port is installed
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#
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set ORG_HOME = `dirname $0`/..
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set PORTNAME = `$ORG_HOME/config/guess_port`
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if (-f $ORG_HOME/ports/$PORTNAME/bin/exonerate) then
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echo "+ port $PORTNAME is correctly installed"
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exit 0
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endif
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echo "! port $PORTNAME not installed"
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echo "! Please read README.txt for proper installation"
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exit 1
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@ -14,6 +14,7 @@
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# gnu tar : version >= 1.15
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# gnu make : version >= 3.81
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# gcc and g++ : version >= 3.4.6
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# gawk : version >= 4.0.1
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#
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# note: valid versions of gnu tar and make are in _unix_tools_
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#
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@ -58,7 +58,7 @@ all: repseek install
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repseek: $(OBJ) main_repseek.c
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$(CC) $(CFLAGS) -o $@ $(OBJ) main_repseek.c $(LDFLAGS);
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$(CC) $(CFLAGS) -o $@ $(OBJ) main_repseek.c $(LDFLAGS) $(LDLIBS);
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install: repseek
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