Switch the go_cds script from tcsh to bash

Former-commit-id: 36041f96b5bb1411a4ac6fecccfbc24b9b90baff
Former-commit-id: 6e63fdff4022a2bb895a44eb6009f41d049ba4ae

detectors/cds/bin/go_cds.sh

@@ -0,0 +1,110 @@
+#!/bin/bash
+#
+#                           Annotate CDS 
+#
+#========================================================================================
+#
+#  Annotate CDS
+#
+#  go_cds.sh <FASTAFILE> [DBROOT]
+#
+#		- <FASTAFILE> : The fasta file containing the genome to annotate
+#       - [DBROOT]    : optionnal argument allowing to specify database directory
+#
+#  Results are printed to the standard output
+#
+#========================================================================================
+# usage: go_cds.sh fasta [db_root]
+#
+
+# -- CAUTION -- Works as long than the script 
+#               is not called through a symlink
+THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
+source "${THIS_DIR}/../../../scripts/bash_init.sh"
+
+needarg 1
+
+Fasta=$1; shift
+
+needfile $Fasta
+
+# Genome names is set from the base
+# name of the genome file without its extension
+Genome=$(basename ${Fasta%.*})
+
+# DbRoot is set to its default values except 
+# if the second argument precise another DbRoot
+
+DbRoot="$CDS_DATA_DIR/chlorodb"
+
+if (( $# > 0)) ; then
+  DbRoot="$1"; Shift
+fi
+
+needdir $DbRoot
+needdir $DbRoot/core
+needfile $DbRoot/core/Annot.lst
+needdir $DbRoot/models
+
+assignundef cdsdetection_pass1 yes
+assignundef cdsdetection_pass2 yes
+
+temp=$(mktempdir $(hostname))
+
+AbsGenoFile=$(getAbsolutePath $Fasta)
+pushd $temp >& /dev/null
+ln -s $AbsGenoFile genome.fasta
+popd >& /dev/null
+
+Fasta="$temp/genome.fasta"
+
+#
+# pass1: run exonerate
+#
+
+if [[ "$cdsdetection_pass1" == "yes" ]] ; then
+    for dir in "core" "shell" "dust" ; do
+    if [[ -d $DbRoot/$dir ]] ; then
+        fams=$(ls $DbRoot/$dir/*.clean.fst)
+        loginfo "running pass1:$dir exonerate of $Genome on $DbRoot"
+        for f in $fams ; do
+        tcsh -f $PROG_DIR/do_exonerate.csh $Fasta $f $DbRoot/models $temp
+        done
+    fi
+    done
+
+    cp $temp/genome.cds.fasta $Genome.cds.fasta 
+
+fi
+
+
+#
+# pass2: transsplicing
+#
+
+if [[ "$cdsdetection_pass2" == "yes" ]] ; then
+    $PROG_DIR/do_rps12.sh $Fasta $temp
+fi
+
+#
+# pass3: prokov
+#
+
+# $PROG_DIR/do_prokov.sh $Fasta $Genome.cds.fasta $temp
+
+#
+# end : output on stdout
+#
+
+cat $temp/*.res
+
+# cleanup everything
+
+assignundef TMP_CLEANUP 1
+
+if (( $TMP_CLEANUP != 0 )) ; then
+  loginfo "  cleanup $temp"
+  (\rm -r $temp) >& /dev/null
+fi
+
+exit 0