134 lines
2.9 KiB
Bash
Executable File
134 lines
2.9 KiB
Bash
Executable File
#!/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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if [[ -z "$ANNOT_MAXCPU" ]] ; then
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Threads=$(nproc)
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else
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Threads=$ANNOT_MAXCPU
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fi
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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/sp_chlorodb"
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if (( $# > 0)) ; then
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DbRoot="$1"; Shift
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fi
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AnnotFile="$DbRoot/Annot.lst"
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needdir $DbRoot
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needdir $DbRoot/core
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needfile $AnnotFile
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needdir $DbRoot/models
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assignundef cdsdetection_pass1 yes
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assignundef cdsdetection_pass2 yes
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assignundef cdsdetection_pass3 yes
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temp=$(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" ; do
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if [[ -d $DbRoot/$dir ]] ; then
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fams=$(ls $DbRoot/$dir/*.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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echo tcsh -f $PROG_DIR/do_exonerate.csh Pass1 $Fasta $f $AnnotFile $DbRoot/models $temp
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done
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fi
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done ) | parallel -j $Threads
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mv $temp/genome.cds.fasta $Genome.cds_pass1.fasta
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fi
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#
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# pass2: RPS12 gene with transsplicing
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#
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if [[ "$cdsdetection_pass2" == "yes" ]] ; then
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loginfo "running pass2:rps12 exonerate of $Genome on $DbRoot"
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$PROG_DIR/do_rps12.sh $Fasta $temp
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fi
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#
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# pass3: run exonerate on shell and dust
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#
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if [[ "$cdsdetection_pass3" == "yes" ]] ; then
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(for dir in "shell" ; do
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if [[ -d $DbRoot/$dir ]] ; then
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fams=$(ls $DbRoot/$dir/*.fst)
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loginfo $fams
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loginfo "running pass3:$dir exonerate of $Genome on $DbRoot"
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for f in $fams ; do
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echo tcsh -f $PROG_DIR/do_exonerate.csh Pass3 $Fasta $f $AnnotFile $DbRoot/models $temp
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done
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fi
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done) | parallel -j $Threads
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mv $temp/genome.cds.fasta $Genome.cds_pass2.fasta
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fi
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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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