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March 8, 2016 16:05
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| ##gff-version 3 | |
| ##sequence-region scaffold10_size537661 1 537661 | |
| scaffold10_size537661 AUGUSTUS gene 745 1674 . - 0 ID=95_g3568;Name=RTM1_1;gene_id=95_g3568 | |
| scaffold10_size537661 AUGUSTUS mRNA 745 1674 . - 0 Parent=95_g3568;gene_id=95_g3568;transcript_id=95_g3568.t1;product=Protein RTM1;locus_tag=95_g3568.1;accession=P40113;score=625;evalue=0.0;translation=MSNDSSGSEWELYRYTPSKGAAIALTVLFIVTTLIYSFQVVWDARKASKPEVDNPFDTPVDKCESITAISLGENYKKLTVRSTFSAFIPLFFGCIMEIVGYIARAVSSSNTKEIAPYVIQAVLLLIAPALYAATIYMLFGRLLHVMRCESLMIVSSRFGTSFFVFGDVVSFCLQAAGGGLMATVNGRTTGSNLITAGLVIQIVFFGVFIINEFRFSYSVARVCPFYRHISKKWWFLNLTLMLSSILIMVRSIVRLVEFVEGYDGFIISHEYFIYVFDAVPMLLAAIVFIVGSFFGNIFTTITECQSLKP | |
| scaffold10_size537661 AUGUSTUS exon 748 1674 0.93 - 0 Parent=95_g3568;gene_id=95_g3568;transcript_id=95_g3568.t1 | |
| scaffold10_size537661 AUGUSTUS CDS 748 1674 0.93 - 0 Parent=95_g3568;Name=RTM1_1;gene_id=95_g3568;transcript_id=95_g3568.t1 | |
| scaffold10_size537661 AUGUSTUS gene 2374 4626 . - 0 ID=95_g3569;Name=-;gene_id=95_g3569 | |
| scaffold10_size537661 AUGUSTUS mRNA 2374 4626 . - 0 Parent=95_g3569;gene_id=95_g3569;transcript_id=95_g3569.t1;product=putative transcriptional regulatory protein YER184C;locus_tag=95_g3569.1;accession=P39961;score=311;evalue=4e-92;translation=MIKGDEGNLSFYKQDDHILEQIKILKKSIDILEKLKLSVVTSSEYATNAIADINRQLETLLSFQHVNINSESVRTYKDNGALENQLLDGNYVAFDAFSTFENVSKGKAVDDIFGLYSPISVMSPKGICWLIQQLIVKSREKDTEETVYILLKFLDAGSSSYKWELIAPVYRLQFILIEFFGCKVPFTRNETLKEAIDAIPPSLRSELKEEGGNSIQDSRKLFMYCVKLLGKHFTSSRHLLRNINIFEQFFQVEELLSTLCYTFLENSLNFRLLDAEFLHDLLCFVKQRHWKDNSFIIGGVIAPLCRQVQDLGLSRWEYYLGMNEEHANPLREIWWDTYWWDKWYVVVTGKLPMIDSSTVTCLLPQQIMRLGVDDAMSSWQMLERVDFTYGSLKDHIMFGYIVLSISINDVFSNVLYNRKFTDYRVFSGITALDFKVVEELLTRINGIRKGFTVLKTTVVHELEKSLLDDDVFRFCIHFAYSRISCLRAIGNLLMRFKSIFHGTSSNLISDQIGECDKDILQTTVETFTFILRANDNIKIKEHVRPISEMGLNILLEAVKAPAGIDVYHISLFCGVASLFDRITCSENGAEKQYNHPGRIVLMEITCIFIFVRVCCLVYRQYKKVSKEELMAILTDFDHTTARFCNETLDIRSDLFQHIIRDKKKSDYHRDIIHGIEKVLGRDIITTIESCEREVISSDEYRQAQYMGNVATKDLDYLRYFLNLDIFPELNTDDELWDDLKEIDKYYCSSV | |
| scaffold10_size537661 AUGUSTUS exon 2377 4626 0.97 - 0 Parent=95_g3569;gene_id=95_g3569;transcript_id=95_g3569.t1 | |
| scaffold10_size537661 AUGUSTUS CDS 2377 4626 0.97 - 0 Parent=95_g3569;Name=-;gene_id=95_g3569;transcript_id=95_g3569.t1 | |
| scaffold10_size537661 SignalP:4.1 signal_peptide 15225 15287 . - 0 product=putative signal peptide | |
| scaffold10_size537661 AUGUSTUS gene 16555 17262 . + 0 ID=95_g3574;Name=-;gene_id=95_g3574 | |
| scaffold10_size537661 AUGUSTUS mRNA 16555 17262 . + 0 Parent=95_g3574;gene_id=95_g3574;transcript_id=95_g3574.t1;product=DUP240 protein YHL044W;locus_tag=95_g3574.1;accession=P38727;score=468;evalue=3e-167;translation=MSSELLISDSKPRPEGLRKLCEGETVILPRDITPSKCAYFLKQNIVFISYIFIHIIITIILNRLALSAHGNTLIVILAALLITISLFLLLLLPYLNCSRYKLRCLDDDCKFKLLAEVITHKPNVDLSTWDRIAYDMNQFVYDRRICADRSFFYDGSSCYQVFKKLVATPYLVNSNMNSIDADLEMRSNAATNINDSGNSSLHIELGTYIFKALAVFRNSVDKYWEDKYPEMGVTV | |
| scaffold10_size537661 AUGUSTUS exon 16555 17259 1 + 0 Parent=95_g3574;gene_id=95_g3574;transcript_id=95_g3574.t1 | |
| scaffold10_size537661 AUGUSTUS CDS 16555 17259 1 + 0 Parent=95_g3574;Name=-;gene_id=95_g3574;transcript_id=95_g3574.t1 | |
| scaffold10_size537661 AUGUSTUS gene 17890 19107 . + 0 ID=95_g3575;Name=ECM34;gene_id=95_g3575 | |
| scaffold10_size537661 AUGUSTUS mRNA 17890 19107 . + 0 Parent=95_g3575;gene_id=95_g3575;transcript_id=95_g3575.t1;product=Protein ECM34;locus_tag=95_g3575.1;accession=P38728;score=353;evalue=2e-120;translation=MEGRKSEDEKNEAALVCDVFESSNAKLPKNVFRSSFTWYCYEVINRSAFHIWLLLCLTLIVGWKVFSGIGGRRPSDSNMDGPQTKHKRNPGFLRRHSTIVILVISLAVSFSWEAFKMYRERTFGKQITQFAKEIIKSAPSTDMESWDRVAADFNSYMYENKLWNTEYFFFDGSSCHVAFRRTLLWISSRIDGDYKIEYFRKHPYIEEALKVYFAEVDRKWNLNTSQQLLSNISVGNIKLPGQSCRFKLFHIFKKVMKQRFSQVATVIFFVMSIRSPRNLGFFFTLALFVVLVCSQEWFSFEMNRSCSMKVEHRMQFLSTIISEHQKSDVNCWDQIAKKMNVYLFEQKVSGSDVFFLDGADCERFFERNFLRYLPSRKSSHPDLPIAELLPYIRKADIACAGKQLI | |
| scaffold10_size537661 AUGUSTUS exon 17890 19104 0.97 + 0 Parent=95_g3575;gene_id=95_g3575;transcript_id=95_g3575.t1 | |
| scaffold10_size537661 AUGUSTUS CDS 17890 19104 0.97 + 0 Parent=95_g3575;Name=ECM34;gene_id=95_g3575;transcript_id=95_g3575.t1 |
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| ##gff-version 3 | |
| scaffold10_size537661 AUGUSTUS gene 745 1674 . - 0 ID=95_g3568;Name=RTM1_1;gene_id=95_g3568 | |
| scaffold10_size537661 AUGUSTUS mRNA 745 1674 . - 0 gene_id=95_g3568;Parent=95_g3568;transcript_id=95_g3568.t1;product=Protein RTM1;locus_tag=95_g3568.1;accession=P40113;score=625;evalue=0.0;translation=MSNDSSGSEWELYRYTPSKGAAIALTVLFIVTTLIYSFQVVWDARKASKPEVDNPFDTPVDKCESITAISLGENYKKLTVRSTFSAFIPLFFGCIMEIVGYIARAVSSSNTKEIAPYVIQAVLLLIAPALYAATIYMLFGRLLHVMRCESLMIVSSRFGTSFFVFGDVVSFCLQAAGGGLMATVNGRTTGSNLITAGLVIQIVFFGVFIINEFRFSYSVARVCPFYRHISKKWWFLNLTLMLSSILIMVRSIVRLVEFVEGYDGFIISHEYFIYVFDAVPMLLAAIVFIVGSFFGNIFTTITECQSLKP | |
| scaffold10_size537661 AUGUSTUS exon 748 1674 0.93 - 0 gene_id=95_g3568;Parent=95_g3568;transcript_id=95_g3568.t1 | |
| scaffold10_size537661 AUGUSTUS CDS 748 1674 0.93 - 0 Name=RTM1_1;gene_id=95_g3568;Parent=95_g3568;transcript_id=95_g3568.t1 | |
| scaffold10_size537661 AUGUSTUS gene 2374 4626 . - 0 ID=95_g3569;Name=-;gene_id=95_g3569 | |
| scaffold10_size537661 AUGUSTUS mRNA 2374 4626 . - 0 gene_id=95_g3569;Parent=95_g3569;transcript_id=95_g3569.t1;product=putative transcriptional regulatory protein YER184C;locus_tag=95_g3569.1;accession=P39961;score=311;evalue=4e-92;translation=MIKGDEGNLSFYKQDDHILEQIKILKKSIDILEKLKLSVVTSSEYATNAIADINRQLETLLSFQHVNINSESVRTYKDNGALENQLLDGNYVAFDAFSTFENVSKGKAVDDIFGLYSPISVMSPKGICWLIQQLIVKSREKDTEETVYILLKFLDAGSSSYKWELIAPVYRLQFILIEFFGCKVPFTRNETLKEAIDAIPPSLRSELKEEGGNSIQDSRKLFMYCVKLLGKHFTSSRHLLRNINIFEQFFQVEELLSTLCYTFLENSLNFRLLDAEFLHDLLCFVKQRHWKDNSFIIGGVIAPLCRQVQDLGLSRWEYYLGMNEEHANPLREIWWDTYWWDKWYVVVTGKLPMIDSSTVTCLLPQQIMRLGVDDAMSSWQMLERVDFTYGSLKDHIMFGYIVLSISINDVFSNVLYNRKFTDYRVFSGITALDFKVVEELLTRINGIRKGFTVLKTTVVHELEKSLLDDDVFRFCIHFAYSRISCLRAIGNLLMRFKSIFHGTSSNLISDQIGECDKDILQTTVETFTFILRANDNIKIKEHVRPISEMGLNILLEAVKAPAGIDVYHISLFCGVASLFDRITCSENGAEKQYNHPGRIVLMEITCIFIFVRVCCLVYRQYKKVSKEELMAILTDFDHTTARFCNETLDIRSDLFQHIIRDKKKSDYHRDIIHGIEKVLGRDIITTIESCEREVISSDEYRQAQYMGNVATKDLDYLRYFLNLDIFPELNTDDELWDDLKEIDKYYCSSV | |
| scaffold10_size537661 AUGUSTUS exon 2377 4626 0.97 - 0 gene_id=95_g3569;Parent=95_g3569;transcript_id=95_g3569.t1 | |
| scaffold10_size537661 AUGUSTUS CDS 2377 4626 0.97 - 0 Name=-;gene_id=95_g3569;Parent=95_g3569;transcript_id=95_g3569.t1 | |
| scaffold10_size537661 SignalP:4.1 signal_peptide 15225 15287 . - 0 product=putative signal peptide | |
| scaffold10_size537661 AUGUSTUS gene 16555 17262 . + 0 ID=95_g3574;Name=-;gene_id=95_g3574 | |
| scaffold10_size537661 AUGUSTUS mRNA 16555 17262 . + 0 gene_id=95_g3574;Parent=95_g3574;transcript_id=95_g3574.t1;product=DUP240 protein YHL044W;locus_tag=95_g3574.1;accession=P38727;score=468;evalue=3e-167;translation=MSSELLISDSKPRPEGLRKLCEGETVILPRDITPSKCAYFLKQNIVFISYIFIHIIITIILNRLALSAHGNTLIVILAALLITISLFLLLLLPYLNCSRYKLRCLDDDCKFKLLAEVITHKPNVDLSTWDRIAYDMNQFVYDRRICADRSFFYDGSSCYQVFKKLVATPYLVNSNMNSIDADLEMRSNAATNINDSGNSSLHIELGTYIFKALAVFRNSVDKYWEDKYPEMGVTV | |
| scaffold10_size537661 AUGUSTUS exon 16555 17259 1 + 0 gene_id=95_g3574;Parent=95_g3574;transcript_id=95_g3574.t1 | |
| scaffold10_size537661 AUGUSTUS CDS 16555 17259 1 + 0 Name=-;gene_id=95_g3574;Parent=95_g3574;transcript_id=95_g3574.t1 | |
| scaffold10_size537661 AUGUSTUS gene 17890 19107 . + 0 ID=95_g3575;Name=ECM34;gene_id=95_g3575 | |
| scaffold10_size537661 AUGUSTUS mRNA 17890 19107 . + 0 gene_id=95_g3575;Parent=95_g3575;transcript_id=95_g3575.t1;product=Protein ECM34;locus_tag=95_g3575.1;accession=P38728;score=353;evalue=2e-120;translation=MEGRKSEDEKNEAALVCDVFESSNAKLPKNVFRSSFTWYCYEVINRSAFHIWLLLCLTLIVGWKVFSGIGGRRPSDSNMDGPQTKHKRNPGFLRRHSTIVILVISLAVSFSWEAFKMYRERTFGKQITQFAKEIIKSAPSTDMESWDRVAADFNSYMYENKLWNTEYFFFDGSSCHVAFRRTLLWISSRIDGDYKIEYFRKHPYIEEALKVYFAEVDRKWNLNTSQQLLSNISVGNIKLPGQSCRFKLFHIFKKVMKQRFSQVATVIFFVMSIRSPRNLGFFFTLALFVVLVCSQEWFSFEMNRSCSMKVEHRMQFLSTIISEHQKSDVNCWDQIAKKMNVYLFEQKVSGSDVFFLDGADCERFFERNFLRYLPSRKSSHPDLPIAELLPYIRKADIACAGKQLI | |
| scaffold10_size537661 AUGUSTUS exon 17890 19104 0.97 + 0 gene_id=95_g3575;Parent=95_g3575;transcript_id=95_g3575.t1 | |
| scaffold10_size537661 AUGUSTUS CDS 17890 19104 0.97 + 0 Name=ECM34;gene_id=95_g3575;Parent=95_g3575;transcript_id=95_g3575.t1 |
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| ##gff-version 3 | |
| scaffold10_size537661 AUGUSTUS gene 745 1674 . - 0 ID=95_g3568;Name=RTM1_1;gene_id=95_g3568 | |
| scaffold10_size537661 AUGUSTUS mRNA 2374 4626 . - 0 gene_id=95_g3569;Parent=95_g3569;transcript_id=95_g3569.t1;product=putative transcriptional regulatory protein YER184C;locus_tag=95_g3569.1;accession=P39961;score=311;evalue=4e-92;translation=MIKGDEGNLSFYKQDDHILEQIKILKKSIDILEKLKLSVVTSSEYATNAIADINRQLETLLSFQHVNINSESVRTYKDNGALENQLLDGNYVAFDAFSTFENVSKGKAVDDIFGLYSPISVMSPKGICWLIQQLIVKSREKDTEETVYILLKFLDAGSSSYKWELIAPVYRLQFILIEFFGCKVPFTRNETLKEAIDAIPPSLRSELKEEGGNSIQDSRKLFMYCVKLLGKHFTSSRHLLRNINIFEQFFQVEELLSTLCYTFLENSLNFRLLDAEFLHDLLCFVKQRHWKDNSFIIGGVIAPLCRQVQDLGLSRWEYYLGMNEEHANPLREIWWDTYWWDKWYVVVTGKLPMIDSSTVTCLLPQQIMRLGVDDAMSSWQMLERVDFTYGSLKDHIMFGYIVLSISINDVFSNVLYNRKFTDYRVFSGITALDFKVVEELLTRINGIRKGFTVLKTTVVHELEKSLLDDDVFRFCIHFAYSRISCLRAIGNLLMRFKSIFHGTSSNLISDQIGECDKDILQTTVETFTFILRANDNIKIKEHVRPISEMGLNILLEAVKAPAGIDVYHISLFCGVASLFDRITCSENGAEKQYNHPGRIVLMEITCIFIFVRVCCLVYRQYKKVSKEELMAILTDFDHTTARFCNETLDIRSDLFQHIIRDKKKSDYHRDIIHGIEKVLGRDIITTIESCEREVISSDEYRQAQYMGNVATKDLDYLRYFLNLDIFPELNTDDELWDDLKEIDKYYCSSV | |
| scaffold10_size537661 AUGUSTUS gene 2374 4626 . - 0 ID=95_g3569;Name=-;gene_id=95_g3569 | |
| scaffold10_size537661 AUGUSTUS exon 2377 4626 0.97 - 0 gene_id=95_g3569;Parent=95_g3569;transcript_id=95_g3569.t1 | |
| scaffold10_size537661 AUGUSTUS CDS 2377 4626 0.97 - 0 Name=-;gene_id=95_g3569;Parent=95_g3569;transcript_id=95_g3569.t1 | |
| scaffold10_size537661 SignalP:4.1 signal_peptide 15225 15287 . - 0 product=putative signal peptide | |
| scaffold10_size537661 AUGUSTUS mRNA 16555 17262 . + 0 gene_id=95_g3574;Parent=95_g3574;transcript_id=95_g3574.t1;product=DUP240 protein YHL044W;locus_tag=95_g3574.1;accession=P38727;score=468;evalue=3e-167;translation=MSSELLISDSKPRPEGLRKLCEGETVILPRDITPSKCAYFLKQNIVFISYIFIHIIITIILNRLALSAHGNTLIVILAALLITISLFLLLLLPYLNCSRYKLRCLDDDCKFKLLAEVITHKPNVDLSTWDRIAYDMNQFVYDRRICADRSFFYDGSSCYQVFKKLVATPYLVNSNMNSIDADLEMRSNAATNINDSGNSSLHIELGTYIFKALAVFRNSVDKYWEDKYPEMGVTV | |
| scaffold10_size537661 AUGUSTUS exon 16555 17259 1 + 0 gene_id=95_g3574;Parent=95_g3574;transcript_id=95_g3574.t1 | |
| scaffold10_size537661 AUGUSTUS CDS 16555 17259 1 + 0 Name=-;gene_id=95_g3574;Parent=95_g3574;transcript_id=95_g3574.t1 | |
| scaffold10_size537661 AUGUSTUS gene 16555 17262 . + 0 ID=95_g3574;Name=-;gene_id=95_g3574 | |
| scaffold10_size537661 AUGUSTUS mRNA 16555 17262 . + 0 gene_id=95_g3574;Parent=95_g3574;transcript_id=95_g3574.t1;product=DUP240 protein YHL044W;locus_tag=95_g3574.1;accession=P38727;score=468;evalue=3e-167;translation=MSSELLISDSKPRPEGLRKLCEGETVILPRDITPSKCAYFLKQNIVFISYIFIHIIITIILNRLALSAHGNTLIVILAALLITISLFLLLLLPYLNCSRYKLRCLDDDCKFKLLAEVITHKPNVDLSTWDRIAYDMNQFVYDRRICADRSFFYDGSSCYQVFKKLVATPYLVNSNMNSIDADLEMRSNAATNINDSGNSSLHIELGTYIFKALAVFRNSVDKYWEDKYPEMGVTV | |
| scaffold10_size537661 AUGUSTUS exon 16555 17259 1 + 0 gene_id=95_g3574;Parent=95_g3574;transcript_id=95_g3574.t1 | |
| scaffold10_size537661 AUGUSTUS CDS 16555 17259 1 + 0 Name=-;gene_id=95_g3574;Parent=95_g3574;transcript_id=95_g3574.t1 | |
| scaffold10_size537661 AUGUSTUS gene 17890 19107 . + 0 ID=95_g3575;Name=ECM34;gene_id=95_g3575 | |
| scaffold10_size537661 AUGUSTUS mRNA 17890 19107 . + 0 gene_id=95_g3575;Parent=95_g3575;transcript_id=95_g3575.t1;product=Protein ECM34;locus_tag=95_g3575.1;accession=P38728;score=353;evalue=2e-120;translation=MEGRKSEDEKNEAALVCDVFESSNAKLPKNVFRSSFTWYCYEVINRSAFHIWLLLCLTLIVGWKVFSGIGGRRPSDSNMDGPQTKHKRNPGFLRRHSTIVILVISLAVSFSWEAFKMYRERTFGKQITQFAKEIIKSAPSTDMESWDRVAADFNSYMYENKLWNTEYFFFDGSSCHVAFRRTLLWISSRIDGDYKIEYFRKHPYIEEALKVYFAEVDRKWNLNTSQQLLSNISVGNIKLPGQSCRFKLFHIFKKVMKQRFSQVATVIFFVMSIRSPRNLGFFFTLALFVVLVCSQEWFSFEMNRSCSMKVEHRMQFLSTIISEHQKSDVNCWDQIAKKMNVYLFEQKVSGSDVFFLDGADCERFFERNFLRYLPSRKSSHPDLPIAELLPYIRKADIACAGKQLI | |
| scaffold10_size537661 AUGUSTUS exon 17890 19104 0.97 + 0 gene_id=95_g3575;Parent=95_g3575;transcript_id=95_g3575.t1 | |
| scaffold10_size537661 AUGUSTUS CDS 17890 19104 0.97 + 0 Name=ECM34;gene_id=95_g3575;Parent=95_g3575;transcript_id=95_g3575.t1 |
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| import gffutils | |
| import os | |
| def writeGFF(gffutilsDB, outputFilename): | |
| with open(outputFilename, 'w') as fout: | |
| fout.write('##gff-version 3' + '\n') | |
| for feature in gffutilsDB.all_features(order_by=('seqid','start')): | |
| fout.write(str(feature) + '\n') | |
| return | |
| def gffExtract(): | |
| genomeGFF = 'test-small.gff' | |
| genomeGFFdb = 'test-small.db' | |
| db = gffutils.create_db(genomeGFF, dbfn=genomeGFFdb, force=True, keep_order=True, merge_strategy="warning") | |
| writeGFF(db, "test-unchanged.gff") | |
| def generatorModifyFeatures(featureFamilies): | |
| for featureFamily in featureFamilies: | |
| # featureFamily[0] is the parent (featureType "gene") | |
| if featureFamily[0].attributes["Name"][0] == "-": | |
| for feature in featureFamily: | |
| print feature | |
| yield feature | |
| featureFamilies = list(db.iter_by_parent_childs()) | |
| db.update(generatorModifyFeatures(featureFamilies), merge_strategy="replace") | |
| writeGFF(db, "test-updated.gff") | |
| gffExtract() |
Also, "test-unchanged.gff" and "test-updated.gff" turn out the same when I just use:
def generatorModifyFeatures(featureFamilies):
for featureFamily in featureFamilies:
for feature in featureFamily:
yield feature
The input file ("test-small.gff") validates according to http://genometools.org/cgi-bin/gff3validator.cgi.
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Difference between "test-unchanged.gff" (left) and "test-updated.gff" (right):