Eric Coissac
4f18ef51d0
Former-commit-id: e6ce2c7387b5abd0ef3be9b58c23bbfe596a5aff Former-commit-id: 85e9495c91660380d531efb63a8f81aa393805cf
114 lines
2.0 KiB
Tcsh
Executable File
114 lines
2.0 KiB
Tcsh
Executable File
#!/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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#
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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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