Explore, edit and leverage genomic annotations using Python GTF toolkit.
Identifieur interne : 000279 ( PubMed/Corpus ); précédent : 000278; suivant : 000280Explore, edit and leverage genomic annotations using Python GTF toolkit.
Auteurs : F. Lopez ; G. Charbonnier ; Y. Kermezli ; M. Belhocine ; Q. Ferré ; N. Zweig ; M. Aribi ; A. Gonzalez ; S. Spicuglia ; D. PuthierSource :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2019.
English descriptors
- KwdEn :
- MESH :
Abstract
MOTIVATION
While Python has become very popular in bioinformatics, a limited number of libraries exist for fast manipulation of gene coordinates in Ensembl GTF format.
RESULTS
We have developed the GTF toolkit Python package (pygtftk), which aims at providing easy and powerful manipulation of gene coordinates in GTF format. For optimal performances, the core engine of pygtftk is a C dynamic library (libgtftk) while the Python API provides usability and readability for developing scripts. Based on this Python package, we have developed the gtftk command line interface that contains 57 sub-commands (v0.9.10) to ease handling of GTF files. These commands may be used to (i) perform basic tasks (e.g. selections, insertions, updates or deletions of features/keys), (ii) select genes/transcripts based on various criteria (e.g. size, exon number, transcription start site location, intron length, GO terms) or (iii) carry out more advanced operations such as coverage analyses of genomic features using bigWig files to create faceted read-coverage diagrams. In conclusion, the pygtftk package greatly simplifies the annotation of GTF files with external information while providing advance tools to perform gene analyses.
AVAILABILITY AND IMPLEMENTATION
pygtftk and gtftk have been tested on Linux and MacOSX and are available from https://github.com/dputhier/pygtftk under the MIT license. The libgtftk dynamic library written in C is available from https://github.com/dputhier/libgtftk.
DOI: 10.1093/bioinformatics/btz116
PubMed: 30768152
Links to Exploration step
pubmed:30768152Le document en format XML
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Kermezli</name><affiliation><nlm:affiliation>Aix Marseille Univ, INSERM, TAGC, UMR U1090, Marseille, France.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>The Laboratory of Applied Molecular Biology and Immunology, Tlemcen University, Algeria.</nlm:affiliation></affiliation></author><author><name sortKey="Belhocine, M" sort="Belhocine, M" uniqKey="Belhocine M" first="M" last="Belhocine">M. Belhocine</name><affiliation><nlm:affiliation>Molecular Biology and Genetics Laboratory, Dubai, United Arab Emirates.</nlm:affiliation></affiliation></author><author><name sortKey="Ferre, Q" sort="Ferre, Q" uniqKey="Ferre Q" first="Q" last="Ferré">Q. Ferré</name><affiliation><nlm:affiliation>Aix Marseille Univ, INSERM, TAGC, UMR U1090, Marseille, France.</nlm:affiliation></affiliation></author><author><name sortKey="Zweig, N" sort="Zweig, N" uniqKey="Zweig N" first="N" last="Zweig">N. Zweig</name><affiliation><nlm:affiliation>Aix Marseille Univ.</nlm:affiliation></affiliation></author><author><name sortKey="Aribi, M" sort="Aribi, M" uniqKey="Aribi M" first="M" last="Aribi">M. Aribi</name><affiliation><nlm:affiliation>The Laboratory of Applied Molecular Biology and Immunology, Tlemcen University, Algeria.</nlm:affiliation></affiliation></author><author><name sortKey="Gonzalez, A" sort="Gonzalez, A" uniqKey="Gonzalez A" first="A" last="Gonzalez">A. Gonzalez</name><affiliation><nlm:affiliation>Aix Marseille Univ, INSERM, TAGC, UMR U1090, Marseille, France.</nlm:affiliation></affiliation></author><author><name sortKey="Spicuglia, S" sort="Spicuglia, S" uniqKey="Spicuglia S" first="S" last="Spicuglia">S. Spicuglia</name><affiliation><nlm:affiliation>Aix Marseille Univ, INSERM, TAGC, UMR U1090, Marseille, France.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Equipe Labellisée LIGUE contre le Cancer.</nlm:affiliation></affiliation></author><author><name sortKey="Puthier, D" sort="Puthier, D" uniqKey="Puthier D" first="D" last="Puthier">D. Puthier</name><affiliation><nlm:affiliation>Aix Marseille Univ, INSERM, TAGC, UMR U1090, Marseille, France.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2019">2019</date><idno type="RBID">pubmed:30768152</idno><idno type="pmid">30768152</idno><idno type="doi">10.1093/bioinformatics/btz116</idno><idno type="wicri:Area/PubMed/Corpus">000279</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000279</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Explore, edit and leverage genomic annotations using Python GTF toolkit.</title><author><name sortKey="Lopez, F" sort="Lopez, F" uniqKey="Lopez F" first="F" last="Lopez">F. Lopez</name><affiliation><nlm:affiliation>Aix Marseille Univ, INSERM, TAGC, UMR U1090, Marseille, France.</nlm:affiliation></affiliation></author><author><name sortKey="Charbonnier, G" sort="Charbonnier, G" uniqKey="Charbonnier G" first="G" last="Charbonnier">G. Charbonnier</name><affiliation><nlm:affiliation>Aix Marseille Univ, INSERM, TAGC, UMR U1090, Marseille, France.</nlm:affiliation></affiliation></author><author><name sortKey="Kermezli, Y" sort="Kermezli, Y" uniqKey="Kermezli Y" first="Y" last="Kermezli">Y. Kermezli</name><affiliation><nlm:affiliation>Aix Marseille Univ, INSERM, TAGC, UMR U1090, Marseille, France.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>The Laboratory of Applied Molecular Biology and Immunology, Tlemcen University, Algeria.</nlm:affiliation></affiliation></author><author><name sortKey="Belhocine, M" sort="Belhocine, M" uniqKey="Belhocine M" first="M" last="Belhocine">M. Belhocine</name><affiliation><nlm:affiliation>Molecular Biology and Genetics Laboratory, Dubai, United Arab Emirates.</nlm:affiliation></affiliation></author><author><name sortKey="Ferre, Q" sort="Ferre, Q" uniqKey="Ferre Q" first="Q" last="Ferré">Q. Ferré</name><affiliation><nlm:affiliation>Aix Marseille Univ, INSERM, TAGC, UMR U1090, Marseille, France.</nlm:affiliation></affiliation></author><author><name sortKey="Zweig, N" sort="Zweig, N" uniqKey="Zweig N" first="N" last="Zweig">N. Zweig</name><affiliation><nlm:affiliation>Aix Marseille Univ.</nlm:affiliation></affiliation></author><author><name sortKey="Aribi, M" sort="Aribi, M" uniqKey="Aribi M" first="M" last="Aribi">M. Aribi</name><affiliation><nlm:affiliation>The Laboratory of Applied Molecular Biology and Immunology, Tlemcen University, Algeria.</nlm:affiliation></affiliation></author><author><name sortKey="Gonzalez, A" sort="Gonzalez, A" uniqKey="Gonzalez A" first="A" last="Gonzalez">A. Gonzalez</name><affiliation><nlm:affiliation>Aix Marseille Univ, INSERM, TAGC, UMR U1090, Marseille, France.</nlm:affiliation></affiliation></author><author><name sortKey="Spicuglia, S" sort="Spicuglia, S" uniqKey="Spicuglia S" first="S" last="Spicuglia">S. Spicuglia</name><affiliation><nlm:affiliation>Aix Marseille Univ, INSERM, TAGC, UMR U1090, Marseille, France.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Equipe Labellisée LIGUE contre le Cancer.</nlm:affiliation></affiliation></author><author><name sortKey="Puthier, D" sort="Puthier, D" uniqKey="Puthier D" first="D" last="Puthier">D. Puthier</name><affiliation><nlm:affiliation>Aix Marseille Univ, INSERM, TAGC, UMR U1090, Marseille, France.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Bioinformatics (Oxford, England)</title><idno type="eISSN">1367-4811</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Computational Biology (MeSH)</term><term>Genomics (MeSH)</term><term>Software (MeSH)</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Computational Biology</term><term>Genomics</term><term>Software</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>MOTIVATION</b></p><p>While Python has become very popular in bioinformatics, a limited number of libraries exist for fast manipulation of gene coordinates in Ensembl GTF format.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>We have developed the GTF toolkit Python package (pygtftk), which aims at providing easy and powerful manipulation of gene coordinates in GTF format. For optimal performances, the core engine of pygtftk is a C dynamic library (libgtftk) while the Python API provides usability and readability for developing scripts. Based on this Python package, we have developed the gtftk command line interface that contains 57 sub-commands (v0.9.10) to ease handling of GTF files. These commands may be used to (i) perform basic tasks (e.g. selections, insertions, updates or deletions of features/keys), (ii) select genes/transcripts based on various criteria (e.g. size, exon number, transcription start site location, intron length, GO terms) or (iii) carry out more advanced operations such as coverage analyses of genomic features using bigWig files to create faceted read-coverage diagrams. In conclusion, the pygtftk package greatly simplifies the annotation of GTF files with external information while providing advance tools to perform gene analyses.</p></div><div type="abstract" xml:lang="en"><p><b>AVAILABILITY AND IMPLEMENTATION</b></p><p>pygtftk and gtftk have been tested on Linux and MacOSX and are available from https://github.com/dputhier/pygtftk under the MIT license. The libgtftk dynamic library written in C is available from https://github.com/dputhier/libgtftk.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">30768152</PMID><DateCompleted><Year>2020</Year><Month>06</Month><Day>10</Day></DateCompleted><DateRevised><Year>2020</Year><Month>06</Month><Day>10</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1367-4811</ISSN><JournalIssue CitedMedium="Internet"><Volume>35</Volume><Issue>18</Issue><PubDate><Year>2019</Year><Month>09</Month><Day>15</Day></PubDate></JournalIssue><Title>Bioinformatics (Oxford, England)</Title><ISOAbbreviation>Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>Explore, edit and leverage genomic annotations using Python GTF toolkit.</ArticleTitle><Pagination><MedlinePgn>3487-3488</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/bioinformatics/btz116</ELocationID><Abstract><AbstractText Label="MOTIVATION">While Python has become very popular in bioinformatics, a limited number of libraries exist for fast manipulation of gene coordinates in Ensembl GTF format.</AbstractText><AbstractText Label="RESULTS">We have developed the GTF toolkit Python package (pygtftk), which aims at providing easy and powerful manipulation of gene coordinates in GTF format. For optimal performances, the core engine of pygtftk is a C dynamic library (libgtftk) while the Python API provides usability and readability for developing scripts. Based on this Python package, we have developed the gtftk command line interface that contains 57 sub-commands (v0.9.10) to ease handling of GTF files. These commands may be used to (i) perform basic tasks (e.g. selections, insertions, updates or deletions of features/keys), (ii) select genes/transcripts based on various criteria (e.g. size, exon number, transcription start site location, intron length, GO terms) or (iii) carry out more advanced operations such as coverage analyses of genomic features using bigWig files to create faceted read-coverage diagrams. In conclusion, the pygtftk package greatly simplifies the annotation of GTF files with external information while providing advance tools to perform gene analyses.</AbstractText><AbstractText Label="AVAILABILITY AND IMPLEMENTATION">pygtftk and gtftk have been tested on Linux and MacOSX and are available from https://github.com/dputhier/pygtftk under the MIT license. The libgtftk dynamic library written in C is available from https://github.com/dputhier/libgtftk.</AbstractText><CopyrightInformation>© The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Lopez</LastName><ForeName>F</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Aix Marseille Univ, INSERM, TAGC, UMR U1090, Marseille, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Charbonnier</LastName><ForeName>G</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Aix Marseille Univ, INSERM, TAGC, UMR U1090, Marseille, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kermezli</LastName><ForeName>Y</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Aix Marseille Univ, INSERM, TAGC, UMR U1090, Marseille, France.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>The Laboratory of Applied Molecular Biology and Immunology, Tlemcen University, Algeria.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Belhocine</LastName><ForeName>M</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Molecular Biology and Genetics Laboratory, Dubai, United Arab Emirates.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ferré</LastName><ForeName>Q</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>Aix Marseille Univ, INSERM, TAGC, UMR U1090, Marseille, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zweig</LastName><ForeName>N</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Aix Marseille Univ.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Aribi</LastName><ForeName>M</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>The Laboratory of Applied Molecular Biology and Immunology, Tlemcen University, Algeria.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gonzalez</LastName><ForeName>A</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Aix Marseille Univ, INSERM, TAGC, UMR U1090, Marseille, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Spicuglia</LastName><ForeName>S</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Aix Marseille Univ, INSERM, TAGC, UMR U1090, Marseille, France.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Equipe Labellisée LIGUE contre le Cancer.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Puthier</LastName><ForeName>D</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Aix Marseille Univ, INSERM, TAGC, UMR U1090, Marseille, France.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Bioinformatics</MedlineTA><NlmUniqueID>9808944</NlmUniqueID><ISSNLinking>1367-4803</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="Y">Genomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012984" MajorTopicYN="Y">Software</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>11</Month><Day>12</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2019</Year><Month>01</Month><Day>15</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>02</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>2</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>6</Month><Day>11</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>2</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">30768152</ArticleId><ArticleId IdType="pii">5320559</ArticleId><ArticleId IdType="doi">10.1093/bioinformatics/btz116</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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