Switch the go_cds script from tcsh to bash
Former-commit-id: 36041f96b5bb1411a4ac6fecccfbc24b9b90baff Former-commit-id: 6e63fdff4022a2bb895a44eb6009f41d049ba4ae
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@ -1,115 +0,0 @@
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#!/usr/bin/env tcsh -f
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#
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# Annotate CDS
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#
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#========================================================================================
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#
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# Annotate CDS
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#
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# go_cds.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 standard output
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#
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#========================================================================================
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# usage: go_cds.sh fasta [db_root]
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#
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unsetenv ORG_SOURCED
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setenv ORG_HOME `dirname $0`/../../..
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source $ORG_HOME/scripts/csh_init.sh
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NeedArg 1
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set Fasta = $Argv[1]; Shift
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NeedFile $Fasta
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set Genome = `basename $Fasta:r`
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set DbRoot = $CDS_DATA_DIR/chlorodb
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if ($#Argv > 0) then
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set DbRoot = $Argv[1]; Shift
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endif
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NeedDir $DbRoot/core
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NeedFile $DbRoot/core/Annot.lst
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NeedDir $DbRoot/models
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#
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# run everything into temporary place
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#
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set temp = `hostname`.$$.Genome.tmp
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if (! -d $temp) then
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Notify "making directory $temp"
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mkdir $temp
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endif
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#
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# find the absolute path of the fasta genome file
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#
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echo $Fasta | grep '^/' > /dev/null
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if ( $status == 1 ) then
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set AbsGenoFile = `pwd`/$Fasta
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set DirGenoFile = `dirname $AbsGenoFile`
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set DirGenoFile = `(cd $DirGenoFile;pwd)`
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set AbsGenoFile = $DirGenoFile/`basename $AbsGenoFile`
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else
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set AbsGenoFile = $Fasta
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endif
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pushd $temp >& /dev/null
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ln -s $AbsGenoFile genome.fasta
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popd >& /dev/null
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set Fasta = $temp/genome.fasta
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#
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# pass1: run exonerate
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#
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foreach dir ("core" "shell" "dust")
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if (-d $DbRoot/$dir) then
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set fams = `ls $DbRoot/$dir/*.clean.fst`
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Notify "running pass1:$dir exonerate of $Genome on $DbRoot"
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foreach f ($fams)
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tcsh -f $PROG_DIR/do_exonerate.csh $Fasta $f $DbRoot/models $temp
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end
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endif
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end
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cp $temp/genome.cds.fasta $Genome.cds.fasta
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#
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# pass2: transsplicing
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#
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$PROG_DIR/do_rps12.sh $Fasta > $temp/$Genome.rps12.res
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#
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# pass3: prokov
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#
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# $PROG_DIR/do_prokov.sh $Fasta $Genome.cds.fasta $temp
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#
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# end : output on stdout
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#
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cat $temp/*.res
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# cleanup everything
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AssignUndef TMP_CLEANUP 1
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if ($TMP_CLEANUP != 0) then
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Notify " cleanup $temp"
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(\rm -r $temp) >& /dev/null
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endif
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Exit 0
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110
detectors/cds/bin/go_cds.sh
Executable file
110
detectors/cds/bin/go_cds.sh
Executable file
@ -0,0 +1,110 @@
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#!/bin/bash
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#
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# Annotate CDS
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#
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#========================================================================================
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#
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# Annotate CDS
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#
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# go_cds.sh <FASTAFILE> [DBROOT]
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#
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# - <FASTAFILE> : The fasta file containing the genome to annotate
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# - [DBROOT] : optionnal argument allowing to specify database directory
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#
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# Results are printed to the standard output
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#
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#========================================================================================
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# usage: go_cds.sh fasta [db_root]
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#
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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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THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${THIS_DIR}/../../../scripts/bash_init.sh"
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needarg 1
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Fasta=$1; shift
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needfile $Fasta
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# Genome names is set from the base
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# name of the genome file without its extension
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Genome=$(basename ${Fasta%.*})
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# DbRoot is set to its default values except
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# if the second argument precise another DbRoot
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DbRoot="$CDS_DATA_DIR/chlorodb"
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if (( $# > 0)) ; then
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DbRoot="$1"; Shift
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fi
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needdir $DbRoot
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needdir $DbRoot/core
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needfile $DbRoot/core/Annot.lst
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needdir $DbRoot/models
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assignundef cdsdetection_pass1 yes
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assignundef cdsdetection_pass2 yes
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temp=$(mktempdir $(hostname))
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AbsGenoFile=$(getAbsolutePath $Fasta)
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pushd $temp >& /dev/null
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ln -s $AbsGenoFile genome.fasta
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popd >& /dev/null
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Fasta="$temp/genome.fasta"
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#
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# pass1: run exonerate
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#
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if [[ "$cdsdetection_pass1" == "yes" ]] ; then
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for dir in "core" "shell" "dust" ; do
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if [[ -d $DbRoot/$dir ]] ; then
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fams=$(ls $DbRoot/$dir/*.clean.fst)
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loginfo "running pass1:$dir exonerate of $Genome on $DbRoot"
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for f in $fams ; do
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tcsh -f $PROG_DIR/do_exonerate.csh $Fasta $f $DbRoot/models $temp
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done
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fi
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done
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cp $temp/genome.cds.fasta $Genome.cds.fasta
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fi
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#
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# pass2: transsplicing
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#
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if [[ "$cdsdetection_pass2" == "yes" ]] ; then
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$PROG_DIR/do_rps12.sh $Fasta $temp
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fi
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#
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# pass3: prokov
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#
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# $PROG_DIR/do_prokov.sh $Fasta $Genome.cds.fasta $temp
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#
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# end : output on stdout
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#
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cat $temp/*.res
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# cleanup everything
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assignundef TMP_CLEANUP 1
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if (( $TMP_CLEANUP != 0 )) ; then
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loginfo " cleanup $temp"
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(\rm -r $temp) >& /dev/null
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fi
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exit 0
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@ -25,8 +25,16 @@ function getAbsolutePath {
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# Manage temp directory
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function pushTmpDir {
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function mktempdir {
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local TMP_DIR
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TMP_DIR=$(mktemp -d -t "$1_proc_$$_XXXXXX")
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logdebug "Creating temp directory $TMP_DIR"
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echo $TMP_DIR
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}
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function pushTmpDir {
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local TMP_DIR
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TMP_DIR=$(mktempdir "$1")
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pushd $TMP_DIR >& /dev/null
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TMP_DIR_STACK="$TMP_DIR $TMP_DIR_STACK"
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logdebug "Pushing temp directory $TMP_DIR"
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@ -34,8 +42,9 @@ function pushTmpDir {
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}
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function popTmpDir {
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TMP_DIR=$(echo $TMP_DIR_STACK | $AwkCmd '{print $1}')
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TMP_DIR_STACK=$(echo $TMP_DIR_STACK | $AwkCmd '{$1="";print $0}')
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local TMP_DIR
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TMP_DIR=$($AwkCmd '{print $1}' <<< $TMP_DIR_STACK)
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TMP_DIR_STACK=$($AwkCmd '{$1="";print $0}' <<< $TMP_DIR_STACK)
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popd >& /dev/null
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rm -rf $TMP_DIR >& /dev/null
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logdebug "Poping temp directory $TMP_DIR"
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@ -86,6 +95,42 @@ function logdebug {
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fi
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}
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#
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# Asserts that the number of arguments passed to the script
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# is at least equal to the first argument of the function.
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#
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# needarg 3
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#
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# requires that the script is called at least with 3 arguments
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#
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__ORG_ANNOT_ARGS_SCRIPT_COUNT__=$#
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function needarg {
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if (( $__ORG_ANNOT_ARGS_SCRIPT_COUNT__ < $1 )) ; then
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logerror "not enougth arguments provided"
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exit 1
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fi
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}
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function needfile {
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if [[ ! -e $1 ]] ; then
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logerror "File $1 doesn't exist"
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exit 1
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fi
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}
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function needdir {
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if [[ ! -d $1 ]] ; then
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logerror "Directory $1 doesn't exist"
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exit 1
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fi
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}
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function assignundef {
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local value=$(eval echo \${$1+x})
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if [[ -z "$value" ]] ; then
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eval $1=$2
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fi
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}
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# Sequence related functions
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# Counts how many sequences are stored in a fasta file
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