Adds changes to conform with EMBL template files
Former-commit-id: 93da2c4c6fe0ca46de5adb439341e970ba5abd55 Former-commit-id: 0ba15a4167e769b8e13507bd399892eb6098b4c8
This commit is contained in:
@ -50,7 +50,7 @@ pushTmpDir ORG.its
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if [[ ${#TSU[@]}=="2" ]] ; then
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if [[ ${#TSU[@]}=="2" ]] ; then
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echo "FT rRNA ${TSU[0]}..${TSU[1]}"
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echo "FT rRNA ${TSU[0]}..${TSU[1]}"
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echo 'FT /gene="5.8S rRNA"'
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echo 'FT /gene="5.8S rRNA"'
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echo 'FT /product="5.8S ribosomal nuclear RNA"'
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echo 'FT /product="5.8S ribosomal RNA"'
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fi
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fi
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if [[ ${#ITS2[@]}=="2" ]] ; then
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if [[ ${#ITS2[@]}=="2" ]] ; then
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@ -61,22 +61,25 @@ pushTmpDir ORG.its
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hmmsearch --max ${RRNADB} ${QUERY} | \
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hmmsearch --max ${RRNADB} ${QUERY} | \
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$AwkCmd '/Query: / { \
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$AwkCmd '/Query: / {
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profil=$2; \
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profil=$2
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match($3,"[0-9][0-9]*");\
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match($3,"[0-9][0-9]*");
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lprof=substr($3,RSTART,RLENGTH)} \
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lprof=substr($3,RSTART,RLENGTH)}
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/ [0-9][0-9]* ! / { \
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/ [0-9][0-9]* ! / {
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print profil,lprof,$7,$8,$10,$11}' | \
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print profil,lprof,$7,$8,$10,$11}' | \
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$AwkCmd '($3 <=5) && (($2-$4) <=5) { \
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$AwkCmd '($3 <=5) && (($2-$4) <=5) {
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full=1;$5=$5-$3+1;$6=$6+($2-$4)} \
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full=1;$5=$5-$3+1;$6=$6+($2-$4)
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{loc=$5".."$6} \
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}
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($1 ~ /_RC$/) { \
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{ loc=$5".."$6 }
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loc="complement("loc")"} \
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($1 ~ /_RC$/) {
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(full==1) {match($1,"_..*S");\
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loc="complement("loc")"
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rrna=substr($1,RSTART+1,RLENGTH-1);\
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}
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print "FT rRNA " loc; \
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(full==1) {
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print "FT /gene=\"rrn"rrna"\""
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match($1,"_..*S")
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print "FT /product=\""rrna" ribosomal RNA\"";\
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rrna=substr($1,RSTART+1,RLENGTH-1)
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print "FT rRNA " loc
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print "FT /gene=\""rrna" rRNA\""
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print "FT /product=\""rrna" ribosomal RNA\""
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full=0
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full=0
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}'
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}'
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247
org-annotate.sh
247
org-annotate.sh
@ -4,8 +4,23 @@
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#
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#
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# Annotate Organelle
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# Annotate Organelle
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#
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#
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# The org-annotate pipeline aims to annotate fasta files produced by assembling
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# genome skimming. It has been developped in the context of the PhyloAlps
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# (http://phyloalps.org) and of the PhyloNorway (http://phylonorway.no) projects.
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#
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# Today it is able to produce EMBL flat files suitable for submission to ENA/EBI
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# It provides annotation procedure for :
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#
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# - Plant chloroplast genomes.
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# - Nuclear rDNA Region.
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#
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#
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#========================================================================================
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#========================================================================================
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#
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#
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# The template used for generating the EMBL files follows the recommendation presented
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# at ENA documentation website (at the date of 2021-11-04).
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#
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# https://ena-docs.readthedocs.io/en/latest/submit/fileprep/sequence-flatfile.html
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#
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#
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#========================================================================================
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#========================================================================================
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@ -27,7 +42,12 @@ cdsdetection_pass1="yes"
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cdsdetection_pass2="yes"
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cdsdetection_pass2="yes"
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trnadetection="yes"
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trnadetection="yes"
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rrnadetection="yes"
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rrnadetection="yes"
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idprefix="no"
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organism="no"
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organism="no"
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country="no"
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specimen="no"
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project="no"
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resetorganism="yes"
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types="chloro"
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types="chloro"
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partial=0
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partial=0
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minlength=0
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minlength=0
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@ -40,16 +60,8 @@ function usage {
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echo ' [-c|--chloroplast|-r|--nuclear-rdna|-m|--mitochondrion] <FASTAFILE>'
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echo ' [-c|--chloroplast|-r|--nuclear-rdna|-m|--mitochondrion] <FASTAFILE>'
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echo
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echo
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echo "Options:"
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echo "Options:"
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echo ' -t ### | --ncbi-taxid ###'
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echo ' ### represents the ncbi taxid associated to the sequence'
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echo
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echo ' -i | --no-ir-detection'
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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 ' -o | --organism <organism_name>'
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echo ' Allows for specifiying the organism name in the embl generated file'
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echo ' Spaces have to be substituted by underscore ex : Abies_alba'
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echo
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echo
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echo ' Defining the sequence category'
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echo ' -c | --chloroplast'
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echo ' -c | --chloroplast'
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echo ' Selects for the annotation of a chloroplast genome'
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echo ' Selects for the annotation of a chloroplast genome'
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echo ' This is the default mode'
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echo ' This is the default mode'
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@ -57,15 +69,53 @@ function usage {
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echo ' -r | --nuclear-rdna'
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echo ' -r | --nuclear-rdna'
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echo ' Selects for the annotation of the rDNA nuclear cistron'
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echo ' Selects for the annotation of the rDNA nuclear cistron'
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echo
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echo
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echo ' -m | --mitochondrion'
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# echo ' -m | --mitochondrion'
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echo ' Selects for the annotation of an animal mitochondrion genome'
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# echo ' Selects for the annotation of an animal mitochondrion genome'
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echo
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echo
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echo ' Providing information about the sequence'
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echo ' -s | --specimen ###'
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echo ' Represents the specimen voucher identifier '
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echo ' (e.g. for herbarium sample TROM_V_991090'
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echo ' will be added to the /specimen_voucher qualifier'
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echo
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echo ' -t | --ncbi-taxid ###'
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echo ' Represents the ncbi taxid associated to the sequence'
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echo
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echo ' -o | --organism <organism_name>'
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echo ' Allows for specifiying the organism name in the embl generated file'
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echo ' Spaces have to be substituted by underscore ex : Abies_alba'
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echo
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echo ' -b | --country "<country_value>[:<region>][, <locality>]"'
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echo ' Location (at least country) of collection'
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echo
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echo ' -f | --not-force-ncbi'
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echo ' Do not force the name of the organism to match the NCBI scientific name.'
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echo ' if the provided NCB taxid is publically defined'
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echo
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echo ' Information related to an ENA project'
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echo ' -P | --project <ENA Project>'
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echo ' The accession number of the related project in ENA'
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echo
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echo ' -i | --id-prefix <prefix>'
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echo ' prefix used to build the sequence identifier'
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echo ' the number of the contig is append to the prefix'
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echo ' to build the complete id. This id is used only if'
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echo ' an ENA project is specified.'
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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 ' -p | --partial'
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echo ' Indicates that the genome sequence is partial and therefore in several contigs'
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echo ' Indicates that the genome sequence is partial and therefore in several contigs'
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echo
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echo
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echo ' -l | --min-length'
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echo ' -l | --min-length'
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echo ' Indicates for partial mode the minimum length of contig to annotate'
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echo ' Indicates for partial mode the minimum length of contig to annotate'
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echo
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echo
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echo ' Setting up the sequence annotation'
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echo ' -N | --no-normalization'
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echo ' Does not normalize the sequence befire annotation'
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echo
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echo ' -I | --no-ir-detection'
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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 ' -C | --no-cds'
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echo ' Do not annotate CDS'
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echo ' Do not annotate CDS'
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echo
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echo
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@ -84,6 +134,59 @@ function usage {
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}
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}
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function ncbiscientificname {
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local efetch='https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi'
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local params='db=taxonomy&id='$1'&mode=text&report=xml'
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local url="${efetch}?${params}"
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curl $url \
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| grep '<ScientificName>' \
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| sed 's/<ScientificName>//' \
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| sed 's@</ScientificName>@@' \
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| sed 's@^ *@@' \
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| sed 's@ *$@@' \
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| head -1
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}
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function split80 {
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local text=$1
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local pattern
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local header
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if (( $# >= 2 )) ; then
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header=$2
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else
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header=""
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fi
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if (( $# >= 3 )) ; then
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pattern=$3
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else
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pattern=" "
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fi
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echo $text \
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| $AwkCmd -v pattern="$pattern" -v header="$header" '
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BEGIN { line = header }
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{
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n = split($0,parts,pattern)
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j = 1
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for (i = 1; i <= n; i++) {
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if (length(line) + length(parts[i]) > 79) {
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print line
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line = header
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j = i
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}
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if (i > j) line = line pattern
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line = line parts[i]
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}
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$0 = line
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}
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END {
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print $0
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}
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'
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}
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function fastaIterator() {
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function fastaIterator() {
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$AwkCmd '/^>/ {if (seq) printf("%s\f",seq); seq=""} \
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$AwkCmd '/^>/ {if (seq) printf("%s\f",seq); seq=""} \
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{if (seq) seq=seq"\n"; seq=seq $1} \
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{if (seq) seq=seq"\n"; seq=seq $1} \
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@ -91,7 +194,7 @@ function fastaIterator() {
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}
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}
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# options may be followed by one colon to indicate they have a required argument
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# options may be followed by one colon to indicate they have a required argument
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if ! options=$(getopt -o t:o:icrmhpl:CDETR -l ncbi-taxid:,organism,no-ir-detection,chloroplast,nuclear-rdna,mitochondrion,partial,min-length:,help,no-cds,no-cds-pass1,no-cds-pass2,no-trna,no-rrna -- "$@")
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if ! options=$(getopt -o s:t:o:b:P:i:fcrmhpl:NICDETR -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 -- "$@")
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then
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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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# something went wrong, getopt will put out an error message for us
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usage $0 1
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usage $0 1
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@ -102,15 +205,21 @@ eval set -- "$options"
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while [ $# -gt 0 ]
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while [ $# -gt 0 ]
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do
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do
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case $1 in
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case $1 in
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-t|--ncbi-taxid) taxid="$2" ; shift ;;
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-i|--no-ir-detection) irdetection="no" ;;
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-o|--organism) organism="$2" ; shift ;;
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-c|--chloroplast) types="chloro" ;;
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-c|--chloroplast) types="chloro" ;;
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-r|--nuclear-rdna) types="nucrdna" ;;
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-r|--nuclear-rdna) types="nucrdna" ;;
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-m|--mitochondrion) types="mito" ;;
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# -m|--mitochondrion) types="mito" ;;
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-t|--ncbi-taxid) taxid="$2" ; shift ;;
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-s|--specimen) specimen="$2" ; shift ;;
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-b|--country) country="$2" ; shift ;;
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-o|--organism) organism="$2" ; shift ;;
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-P|--project) project="$2" ; shift ;;
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-i|--id-prefix) idprefix="$2" ; shift ;;
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-f|--not-force-ncbi) resetorganism="no" ;;
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-p|--partial) partial="1" ;;
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-p|--partial) partial="1" ;;
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-l|--min-length) minlength="$2" ; shift ;;
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-l|--min-length) minlength="$2" ; shift ;;
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-h|--help) usage $0 0;;
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-h|--help) usage $0 0;;
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-N|--no-normalization) normalization="no" ;;
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-I|--no-ir-detection) irdetection="no" ;;
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-C|--no-cds) cdsdetection="no";;
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-C|--no-cds) cdsdetection="no";;
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-D|--no-cds-pass1) cdsdetection_pass1="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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-E|--no-cds-pass2) cdsdetection_pass2="no";;
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@ -123,16 +232,33 @@ do
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shift
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shift
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done
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done
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loginfo "Annotating mode.....: $types"
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loginfo "NCBI taxid provided......: $taxid"
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loginfo "IR detection mode...: $irdetection"
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loginfo "CDS detection mode..: $cdsdetection"
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if [[ "$taxid" != "no" ]] ; then
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loginfo " pass 1...: $cdsdetection_pass1"
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scientificname=$(ncbiscientificname $taxid)
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loginfo " pass 2...: $cdsdetection_pass2"
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loginfo "NCBI scientific name.....: $scientificname"
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loginfo "tRNA detection mode.: $trnadetection"
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if [[ -z "$scientificname" ]] ; then
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loginfo "rRNA detection mode.: $rrnadetection"
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loginfo " Unknown taxid."
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loginfo "Organism............: $organism"
|
else
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loginfo "Partial mode........: $partial"
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loginfo "Organism name from taxid.: $resetorganism"
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loginfo "Minimum length......: $minlength"
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if [[ "$resetorganism" == "yes" ]] ; then
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organism=$(echo $scientificname | tr ' ' '_')
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|
fi
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fi
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fi
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loginfo "Annotating mode..........: $types"
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loginfo "Sequence normalization...: $normalization"
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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 "tRNA detection mode......: $trnadetection"
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|
loginfo "rRNA detection mode......: $rrnadetection"
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loginfo "Organism.................: $organism"
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loginfo "Country..................: $country"
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loginfo "Partial mode.............: $partial"
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loginfo "Minimum length...........: $minlength"
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|
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#############################
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#############################
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@ -156,7 +282,10 @@ pushTmpDir ORG.organnot
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|
|
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IFS=$'\f'
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IFS=$'\f'
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|
|
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sequence_number=0
|
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|
|
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for sequence in $(fastaIterator "${QUERY}") ; do
|
for sequence in $(fastaIterator "${QUERY}") ; do
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|
let sequence_number=sequence_number+1
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unset IFS
|
unset IFS
|
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if [[ ! -z "${sequence}" ]] ; then
|
if [[ ! -z "${sequence}" ]] ; then
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echo "${sequence}" > toannotate.fasta
|
echo "${sequence}" > toannotate.fasta
|
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@ -172,10 +301,15 @@ pushTmpDir ORG.organnot
|
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|
|
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if [[ "$irdetection" == "yes" ]] && (( partial == 0 )) ; then
|
if [[ "$irdetection" == "yes" ]] && (( partial == 0 )) ; then
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|
|
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|
if [[ "$normalization" == "yes" ]] ; then
|
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loginfo "Normalizing the structure of the Chloroplast sequence..."
|
loginfo "Normalizing the structure of the Chloroplast sequence..."
|
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loginfo " LSC + IRB + SSC + IRA"
|
loginfo " LSC + IRB + SSC + IRA"
|
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${PROG_DIR}/detectors/normalize/bin/go_normalize.sh toannotate.fasta > "${RESULTS}.norm.fasta"
|
${PROG_DIR}/detectors/normalize/bin/go_normalize.sh toannotate.fasta > "${RESULTS}.norm.fasta"
|
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loginfo "Done."
|
loginfo "Done."
|
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|
else
|
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|
loginfo "No normalization the structure of the Chloroplast sequence..."
|
||||||
|
cat toannotate.fasta > "${RESULTS}.norm.fasta"
|
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|
fi
|
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|
|
||||||
loginfo "Annotating the Inverted repeats and Single copies (LSC and SSC)..."
|
loginfo "Annotating the Inverted repeats and Single copies (LSC and SSC)..."
|
||||||
${PROG_DIR}/detectors/ir/bin/go_ir.sh "${RESULTS}.norm.fasta" > "${RESULTS}.annot"
|
${PROG_DIR}/detectors/ir/bin/go_ir.sh "${RESULTS}.norm.fasta" > "${RESULTS}.annot"
|
||||||
@ -220,16 +354,40 @@ pushTmpDir ORG.organnot
|
|||||||
nucrdna)
|
nucrdna)
|
||||||
loginfo "Annotating a plant rDNA cistron..."
|
loginfo "Annotating a plant rDNA cistron..."
|
||||||
|
|
||||||
|
if [[ "$normalization" == "yes" ]] ; then
|
||||||
loginfo "Normalizing the structure of the cistron sequence..."
|
loginfo "Normalizing the structure of the cistron sequence..."
|
||||||
${PROG_DIR}/detectors/normalizerdna/bin/go_normalizerdna.sh toannotate.fasta > "${RESULTS}.norm.fasta"
|
${PROG_DIR}/detectors/normalizerdna/bin/go_normalizerdna.sh toannotate.fasta > "${RESULTS}.norm.fasta"
|
||||||
loginfo "Done."
|
loginfo "Done."
|
||||||
|
else
|
||||||
|
loginfo "No normalization of the structure of the cistron sequence..."
|
||||||
|
cat toannotate.fasta > "${RESULTS}.norm.fasta"
|
||||||
|
fi
|
||||||
|
|
||||||
loginfo "Annotating the rRNA genes..."
|
loginfo "Annotating the rRNA genes..."
|
||||||
${PROG_DIR}/detectors/nucrrna/bin/go_nucrrna.sh "${RESULTS}.norm.fasta" > "${RESULTS}.annot"
|
${PROG_DIR}/detectors/nucrrna/bin/go_nucrrna.sh "${RESULTS}.norm.fasta" > "${RESULTS}.annot"
|
||||||
loginfo "Done."
|
loginfo "Done."
|
||||||
|
|
||||||
topology="linear"
|
topology="linear"
|
||||||
defline="18S rRNA gene, ITS1, 5.8S rRNA gene, ITS2 and 28S rRNA gene"
|
defline=$(cat "${RESULTS}.annot" \
|
||||||
|
| grep "/gene=" \
|
||||||
|
| sed -E 's@^FT */gene="([^"]*)".*$@\1@' \
|
||||||
|
| sort -u \
|
||||||
|
| awk '{printf("%s;",$0)}' \
|
||||||
|
| awk 'BEGIN {i=1}
|
||||||
|
/18S rRNA;/ {gene[i]="18S rRNA"; i++}
|
||||||
|
/ITS1;/ {gene[i]="ITS1"; i++}
|
||||||
|
/5.8S rRNA;/ {gene[i]="5.8S rRNA"; i++}
|
||||||
|
/ITS2;/ {gene[i]="ITS2"; i++}
|
||||||
|
/28S rRNA;/ {gene[i]="28S rRNA"; ii++}
|
||||||
|
END {
|
||||||
|
for (i=1;i <= length(gene); i++) {
|
||||||
|
separator =""
|
||||||
|
if (i < (length(gene)-1)) separator=", "
|
||||||
|
if (i == (length(gene)-1)) separator=" and "
|
||||||
|
printf("%s gene%s",gene[i],separator)
|
||||||
|
}
|
||||||
|
}')
|
||||||
|
# defline="18S rRNA gene, ITS1, 5.8S rRNA gene, ITS2 and 28S rRNA gene"
|
||||||
;;
|
;;
|
||||||
|
|
||||||
mito)
|
mito)
|
||||||
@ -257,13 +415,30 @@ pushTmpDir ORG.organnot
|
|||||||
organism="$(echo ${organism} | tr '_' ' ')"
|
organism="$(echo ${organism} | tr '_' ' ')"
|
||||||
fi
|
fi
|
||||||
|
|
||||||
|
if [[ "$specimen" != "no" ]] ; then
|
||||||
|
defline="${defline}, voucher ${specimen}"
|
||||||
|
fi
|
||||||
|
|
||||||
sl=$(seqlength "${RESULTS}.norm.fasta")
|
sl=$(seqlength "${RESULTS}.norm.fasta")
|
||||||
|
|
||||||
loginfo "Printing minimal header..."
|
loginfo "Printing minimal header..."
|
||||||
echo "ID ${seqid}; ${seqid}; ${topology}; genomic DNA; XXX; XXX; ${sl} BP."
|
echo "ID XXX; XXX; ${topology}; genomic DNA; XXX; XXX; ${sl} BP."
|
||||||
echo "XX"
|
echo "XX"
|
||||||
echo "AC ${seqid};"
|
echo "AC XXX;"
|
||||||
echo "DE ${organism} ${defline}."
|
echo "XX"
|
||||||
|
if [[ "${project}" != "no" ]] ; then
|
||||||
|
sequence_number
|
||||||
|
if [[ "$idprefix" != "no" ]] ; then
|
||||||
|
seqid="${idprefix}${sequence_number}"
|
||||||
|
fi
|
||||||
|
echo "AC * _${seqid};"
|
||||||
|
echo "XX"
|
||||||
|
echo "PR Project:${project};"
|
||||||
|
echo "XX"
|
||||||
|
fi
|
||||||
|
|
||||||
|
split80 "${organism} ${defline}." "DE "
|
||||||
|
echo "DE "
|
||||||
echo "XX"
|
echo "XX"
|
||||||
loginfo "Done."
|
loginfo "Done."
|
||||||
|
|
||||||
@ -274,7 +449,7 @@ pushTmpDir ORG.organnot
|
|||||||
loginfo "Printing the source feature"
|
loginfo "Printing the source feature"
|
||||||
echo "FT source 1..${sl}"
|
echo "FT source 1..${sl}"
|
||||||
|
|
||||||
if [[ "${organism}" != "{organism}" ]] ; then
|
if [[ "${organism}" != "no" ]] ; then
|
||||||
echo "FT /organism=\"${organism}\""
|
echo "FT /organism=\"${organism}\""
|
||||||
fi
|
fi
|
||||||
|
|
||||||
@ -292,11 +467,18 @@ pushTmpDir ORG.organnot
|
|||||||
|
|
||||||
echo "FT /mol_type=\"genomic DNA\""
|
echo "FT /mol_type=\"genomic DNA\""
|
||||||
|
|
||||||
|
if [[ "${specimen}" != "no" ]] ; then
|
||||||
|
echo "FT /specimen_voucher=\"${specimen}\""
|
||||||
|
fi
|
||||||
|
|
||||||
if [[ "${taxid}" != "no" ]] ; then
|
if [[ "${taxid}" != "no" ]] ; then
|
||||||
echo "FT /db_xref=\"taxon:${taxid}\""
|
echo "FT /db_xref=\"taxon:${taxid}\""
|
||||||
fi
|
fi
|
||||||
|
|
||||||
# echo "FT /country=\"Poland: Bialowieza Forest\""
|
if [[ "${country}" != "no" ]] ; then
|
||||||
|
echo "FT /country=\"${country}\""
|
||||||
|
fi
|
||||||
|
|
||||||
loginfo "Done."
|
loginfo "Done."
|
||||||
|
|
||||||
loginfo "Ordering annotations..."
|
loginfo "Ordering annotations..."
|
||||||
@ -379,4 +561,5 @@ pushTmpDir ORG.organnot
|
|||||||
IFS=$'\f'
|
IFS=$'\f'
|
||||||
done # End of the loop over the sequences
|
done # End of the loop over the sequences
|
||||||
popTmpDir
|
popTmpDir
|
||||||
|
loginfo "Annotation done."
|
||||||
|
|
||||||
|
|||||||
Reference in New Issue
Block a user