Switch to a swissprot based reference database for CDS annotation
Former-commit-id: 3da31ce8a135394ecac041291134d61f11f06d8f Former-commit-id: 406f41a7cb2db14ea832480b86f72a11d3b0ab4a
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@ -40,6 +40,7 @@ irdetection="yes"
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cdsdetection="yes"
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cdsdetection_pass1="yes"
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cdsdetection_pass2="yes"
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cdsdetection_pass3="yes"
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trnadetection="yes"
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rrnadetection="yes"
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idprefix="no"
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@ -53,6 +54,7 @@ resetorganism="yes"
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types="chloro"
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partial=0
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minlength=0
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listfile="no"
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function usage {
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echo "Usage:" ;
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@ -113,6 +115,9 @@ function usage {
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echo ' -S | --locus-shift <###>'
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echo ' Start number for building locus tags'
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echo
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echo ' --list-file <FILENAME>'
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echo ' The chomosome list file name to file for ENA submmission'
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echo
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echo ' Annotation of partial sequences'
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echo ' -p | --partial'
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echo ' Indicates that the genome sequence is partial and therefore in several contigs'
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@ -128,14 +133,17 @@ function usage {
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echo ' Does not look for inverted repeats in the plastid genome'
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echo
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echo ' -C | --no-cds'
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echo ' Do not annotate CDS'
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echo ' Do not annotate CDSs'
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echo
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echo ' -D | --no-cds-pass1'
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echo ' Do not annotate core CDS'
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echo ' Do not annotate core CDSs'
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echo
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echo ' -E | --no-cds-pass2'
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echo ' Do not annotate rps12 CDS'
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echo
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echo ' -F | --no-cds-pass3'
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echo ' Do not annotate shell and dust CDSs'
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echo
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echo ' -T | --no-trna'
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echo ' Do not look for transfert RNA'
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echo
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@ -205,7 +213,7 @@ function fastaIterator() {
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}
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# options may be followed by one colon to indicate they have a required argument
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if ! options=$(getopt -o s:t:o:b:P:i:fcrmhpl:NICDETRL:S: -l specimen:,ncbi-taxid:,organism:,country:,project:,id-prefix:,not-force-ncbi,chloroplast,nuclear-rdna,mitochondrion,partial,min-length:,help,no-normalization,no-ir-detection,no-cds,no-cds-pass1,no-cds-pass2,no-trna,no-rrna,locus-prefix:,locus-shift: -- "$@")
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if ! options=$(getopt -o s:t:o:b:P:i:fcrmhpl:NICDEFTRL:S: -l specimen:,ncbi-taxid:,organism:,country:,project:,id-prefix:,not-force-ncbi,chloroplast,nuclear-rdna,mitochondrion,partial,min-length:,help,no-normalization,no-ir-detection,no-cds,no-cds-pass1,no-cds-pass2,no-cds-pass3,no-trna,no-rrna,locus-prefix:,locus-shift:,list-file: -- "$@")
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then
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# something went wrong, getopt will put out an error message for us
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usage $0 1
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@ -236,8 +244,10 @@ do
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-C|--no-cds) cdsdetection="no";;
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-D|--no-cds-pass1) cdsdetection_pass1="no";;
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-E|--no-cds-pass2) cdsdetection_pass2="no";;
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-F|--no-cds-pass3) cdsdetection_pass3="no";;
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-T|--no-trna) trnadetection="no";;
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-R|--no-rrna) rrnadetection="no";;
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--list-file) listfile="$2" ; shift;;
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(--) shift; break;;
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(-*) echo "$0: error - unrecognized option $1" 1>&2; exit 1;;
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(*) break;;
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@ -249,6 +259,10 @@ loginfo "Locus tag prefix provided: $tagprefix"
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loginfo "Locus tag numbered from..: $locusshift"
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loginfo "NCBI taxid provided......: $taxid"
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if [[ "$listfile" != "no" ]] ; then
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loginfo "contig info saved in.....: $listfile"
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fi
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if [[ "$taxid" != "no" ]] ; then
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scientificname=$(ncbiscientificname $taxid)
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loginfo "NCBI scientific name.....: $scientificname"
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@ -268,6 +282,7 @@ loginfo "IR detection mode........: $irdetection"
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loginfo "CDS detection mode.......: $cdsdetection"
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loginfo " pass 1........: $cdsdetection_pass1"
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loginfo " pass 2........: $cdsdetection_pass2"
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loginfo " pass 3........: $cdsdetection_pass3"
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loginfo "tRNA detection mode......: $trnadetection"
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loginfo "rRNA detection mode......: $rrnadetection"
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loginfo "Organism.................: $organism"
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@ -309,7 +324,8 @@ pushTmpDir ORG.organnot
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if (( sl >= minlength )) ; then
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seqid=$($AwkCmd '(NR==1) {print substr($1,2,1000)}' toannotate.fasta)
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# seqid=$(tr "." "_" <<< ${seqid})
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case "$types" in
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chloro)
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loginfo "Annotating a plant chloroplast genome..."
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@ -351,8 +367,9 @@ pushTmpDir ORG.organnot
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if [[ "$cdsdetection" == "yes" ]] ; then
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loginfo "Annotating the CDS..."
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cdsdetection_pass1=$cdsdetection_pass1 \
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cdsdetection_pass1=$cdsdetection_pass1 \
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cdsdetection_pass2=$cdsdetection_pass2 \
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cdsdetection_pass3=$cdsdetection_pass3 \
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${PROG_DIR}/detectors/cds/bin/go_cds.sh "${RESULTS}.norm.fasta" >> "${RESULTS}.annot"
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loginfo "Done."
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fi
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@ -364,8 +381,19 @@ pushTmpDir ORG.organnot
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topology="linear"
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defline="plastid, partial sequence"
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fi
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if [[ "$listfile" != "no" ]] ; then
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if (( partial == 0 )) ; then
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echo "${seqid} CHL Circular-Chromosome Chloroplast" >> ${CALL_DIR}/$listfile
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else
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echo "${seqid} CHL" >> ${CALL_DIR}/$listfile
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fi
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fi
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notAnnoted "${RESULTS}.annot" "${RESULTS}.norm.fasta" 100 > ${CALL_DIR}/not_annotated.fasta
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;;
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nucrdna)
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loginfo "Annotating a plant rDNA cistron..."
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@ -387,8 +415,8 @@ pushTmpDir ORG.organnot
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| grep "/gene=" \
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| sed -E 's@^FT */gene="([^"]*)".*$@\1@' \
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| sort -u \
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| awk '{printf("%s;",$0)}' \
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| awk 'BEGIN {i=1}
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| $AwkCmd '{printf("%s;",$0)}' \
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| $AwkCmd 'BEGIN {i=1}
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/18S rRNA;/ {gene[i]="18S rRNA"; i++}
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/ITS1;/ {gene[i]="ITS1"; i++}
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/5.8S rRNA;/ {gene[i]="5.8S rRNA"; i++}
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@ -442,7 +470,6 @@ pushTmpDir ORG.organnot
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echo "AC XXX;"
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echo "XX"
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if [[ "${project}" != "no" ]] ; then
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sequence_number
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if [[ "$idprefix" != "no" ]] ; then
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seqid="${idprefix}${sequence_number}"
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fi
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