Commit a16feefc by Eric Coissac

add a -l option to set a minimum length on the contig to annotate

parent 35e27b66
......@@ -25,6 +25,7 @@ irdetection="yes"
organism="no"
types="chloro"
partial=0
minlength=0
function usage {
echo "Usage:" ;
......@@ -56,6 +57,9 @@ function usage {
echo
echo ' -p | --partial'
echo ' Indicates that the genome sequence is partial and therefore in several contigs'
echo
echo ' -l | --min-length'
echo ' Indicates for partial mode the minimum length of contig to annotate'
exit $2
}
......@@ -67,7 +71,7 @@ function fastaIterator() {
}
# options may be followed by one colon to indicate they have a required argument
if ! options=$(getopt -o t:o:icrmhp -l ncbi-taxid:,organism,no-ir-detection,chloroplast,nuclear-rdna,mitochondrion,partial,help -- "$@")
if ! options=$(getopt -o t:o:icrmhpl: -l ncbi-taxid:,organism,no-ir-detection,chloroplast,nuclear-rdna,mitochondrion,partial,min-length:,help -- "$@")
then
# something went wrong, getopt will put out an error message for us
usage $0 1
......@@ -85,6 +89,7 @@ do
-r|--nuclear-rdna) types="nucrdna" ;;
-m|--mitochondrion) types="mito" ;;
-p|--partial) partial="1" ;;
-l|--min-length) minlength="$2" ; shift ;;
-h|--help) usage $0 0;;
(--) shift; break;;
(-*) echo "$0: error - unrecognized option $1" 1>&2; exit 1;;
......@@ -97,6 +102,7 @@ loginfo "Annotating mode.....: $types"
loginfo "IR detection mode...: $irdetection"
loginfo "Organism............: $organism"
loginfo "Partial mode........: $partial"
loginfo "Minimum length......: $minlength"
#############################
......@@ -124,6 +130,9 @@ pushTmpDir ORG.organnot
unset IFS
if [[ ! -z "${sequence}" ]] ; then
echo "${sequence}" > toannotate.fasta
sl=$(seqlength "toannotate.fasta")
if (( sl >= minlength )) ; then
seqid=$($AwkCmd '(NR==1) {print substr($1,2,1000)}' toannotate.fasta)
......@@ -326,7 +335,8 @@ pushTmpDir ORG.organnot
loginfo "Closing sequence part..."
echo "//"
loginfo "Done."
fi
fi # End of the minimum length condition
fi # End of not empty sequence condition
IFS=$'\f'
done # End of the loop over the sequences
......
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