Importing GFF file with Biopython
$begingroup$
Is there a way to import a GFF file for an organism with Biopython in the same way you can for a Genbank file?
For example,
from Bio import Entrez as ez
ez.email = '...'
handle = ez.efetch(db='gene', id='AE015451.2', rettype='genbank', retmode='xml')
h = handle.read()
print(h)
This will import a Gebank xml file for Pseudomonas putida. Is there a way to do this for a GFF file?
biopython ncbi genbank gff
edited Dec 13 '18 at 14:35
Daniel Standage
2,555331
asked Dec 10 '18 at 2:19
Alex SummersAlex Summers
383
$endgroup$
add a comment |
$begingroup$
Is there a way to import a GFF file for an organism with Biopython in the same way you can for a Genbank file?
For example,
from Bio import Entrez as ez
ez.email = '...'
handle = ez.efetch(db='gene', id='AE015451.2', rettype='genbank', retmode='xml')
h = handle.read()
print(h)
This will import a Gebank xml file for Pseudomonas putida. Is there a way to do this for a GFF file?
biopython ncbi genbank gff
edited Dec 13 '18 at 14:35
Daniel Standage
2,555331
asked Dec 10 '18 at 2:19
Alex SummersAlex Summers
383
$endgroup$
add a comment |
$begingroup$
Is there a way to import a GFF file for an organism with Biopython in the same way you can for a Genbank file?
For example,
from Bio import Entrez as ez
ez.email = '...'
handle = ez.efetch(db='gene', id='AE015451.2', rettype='genbank', retmode='xml')
h = handle.read()
print(h)
This will import a Gebank xml file for Pseudomonas putida. Is there a way to do this for a GFF file?
biopython ncbi genbank gff
edited Dec 13 '18 at 14:35
Daniel Standage
2,555331
asked Dec 10 '18 at 2:19
Alex SummersAlex Summers
383
$endgroup$
Is there a way to import a GFF file for an organism with Biopython in the same way you can for a Genbank file?
For example,
from Bio import Entrez as ez
ez.email = '...'
handle = ez.efetch(db='gene', id='AE015451.2', rettype='genbank', retmode='xml')
h = handle.read()
print(h)
This will import a Gebank xml file for Pseudomonas putida. Is there a way to do this for a GFF file?
biopython ncbi genbank gff
biopython ncbi genbank gff
edited Dec 13 '18 at 14:35
Daniel Standage
2,555331
asked Dec 10 '18 at 2:19
Alex SummersAlex Summers
383
edited Dec 13 '18 at 14:35
Daniel Standage
2,555331
asked Dec 10 '18 at 2:19
Alex SummersAlex Summers
383
edited Dec 13 '18 at 14:35
Daniel Standage
2,555331
edited Dec 13 '18 at 14:35
Daniel Standage
2,555331
edited Dec 13 '18 at 14:35
Daniel Standage
2,555331
2,555331
asked Dec 10 '18 at 2:19
Alex SummersAlex Summers
383
asked Dec 10 '18 at 2:19
Alex SummersAlex Summers
383
asked Dec 10 '18 at 2:19
Alex SummersAlex Summers
383
383
add a comment |
add a comment |
3 Answers
3
active
oldest
votes
$begingroup$
No, there is currently no GFF support in biopython.
However, you can read in GFF files into python using this package, gffutils. There are also a few other packages to read/write GFF files, like gff3.
answered Dec 10 '18 at 2:57
conchoeciaconchoecia
2,0101526
$endgroup$
add a comment |
$begingroup$
I would use BCBio for gff handling as it is written to directly interface with BioPython’s object model.
The only downside is that I believe it is no longer actively supported. It is however the package that the BioPython docs use generally. There are plans to properly incorporate GFF/GTF parsers in to BP in the not too distant future according to that link though.
answered Dec 11 '18 at 19:53
Joe HealeyJoe Healey
31517
$endgroup$
add a comment |
$begingroup$
Most GFF parsers handle the work of reading annotation data into objects for convenient data access, but most do not handle the important task of resolving relationships between features. The tag Python library does both, grouping related features together for inspection, traversal, and feature-by-feature processing.
CAVEAT: The tag library only supports GFF3.
DISCLAIMER: I'm the developer of the tag library, so this is a shameless plug. :-)
answered Dec 13 '18 at 14:35
Daniel StandageDaniel Standage
2,555331
$endgroup$
add a comment |
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3 Answers
3
active
oldest
votes
3 Answers
3
active
oldest
votes
active
oldest
votes
active
oldest
votes
$begingroup$
No, there is currently no GFF support in biopython.
However, you can read in GFF files into python using this package, gffutils. There are also a few other packages to read/write GFF files, like gff3.
answered Dec 10 '18 at 2:57
conchoeciaconchoecia
2,0101526
$endgroup$
add a comment |
$begingroup$
No, there is currently no GFF support in biopython.
However, you can read in GFF files into python using this package, gffutils. There are also a few other packages to read/write GFF files, like gff3.
answered Dec 10 '18 at 2:57
conchoeciaconchoecia
2,0101526
$endgroup$
add a comment |
$begingroup$
No, there is currently no GFF support in biopython.
However, you can read in GFF files into python using this package, gffutils. There are also a few other packages to read/write GFF files, like gff3.
answered Dec 10 '18 at 2:57
conchoeciaconchoecia
2,0101526
$endgroup$
No, there is currently no GFF support in biopython.
However, you can read in GFF files into python using this package, gffutils. There are also a few other packages to read/write GFF files, like gff3.
answered Dec 10 '18 at 2:57
conchoeciaconchoecia
2,0101526
answered Dec 10 '18 at 2:57
conchoeciaconchoecia
2,0101526
answered Dec 10 '18 at 2:57
conchoeciaconchoecia
2,0101526
answered Dec 10 '18 at 2:57
conchoeciaconchoecia
2,0101526
2,0101526
add a comment |
add a comment |
$begingroup$
I would use BCBio for gff handling as it is written to directly interface with BioPython’s object model.
The only downside is that I believe it is no longer actively supported. It is however the package that the BioPython docs use generally. There are plans to properly incorporate GFF/GTF parsers in to BP in the not too distant future according to that link though.
answered Dec 11 '18 at 19:53
Joe HealeyJoe Healey
31517
$endgroup$
add a comment |
$begingroup$
I would use BCBio for gff handling as it is written to directly interface with BioPython’s object model.
The only downside is that I believe it is no longer actively supported. It is however the package that the BioPython docs use generally. There are plans to properly incorporate GFF/GTF parsers in to BP in the not too distant future according to that link though.
answered Dec 11 '18 at 19:53
Joe HealeyJoe Healey
31517
$endgroup$
add a comment |
$begingroup$
I would use BCBio for gff handling as it is written to directly interface with BioPython’s object model.
The only downside is that I believe it is no longer actively supported. It is however the package that the BioPython docs use generally. There are plans to properly incorporate GFF/GTF parsers in to BP in the not too distant future according to that link though.
answered Dec 11 '18 at 19:53
Joe HealeyJoe Healey
31517
$endgroup$
I would use BCBio for gff handling as it is written to directly interface with BioPython’s object model.
The only downside is that I believe it is no longer actively supported. It is however the package that the BioPython docs use generally. There are plans to properly incorporate GFF/GTF parsers in to BP in the not too distant future according to that link though.
answered Dec 11 '18 at 19:53
Joe HealeyJoe Healey
31517
answered Dec 11 '18 at 19:53
Joe HealeyJoe Healey
31517
answered Dec 11 '18 at 19:53
Joe HealeyJoe Healey
31517
answered Dec 11 '18 at 19:53
Joe HealeyJoe Healey
31517
31517
add a comment |
add a comment |
$begingroup$
Most GFF parsers handle the work of reading annotation data into objects for convenient data access, but most do not handle the important task of resolving relationships between features. The tag Python library does both, grouping related features together for inspection, traversal, and feature-by-feature processing.
CAVEAT: The tag library only supports GFF3.
DISCLAIMER: I'm the developer of the tag library, so this is a shameless plug. :-)
answered Dec 13 '18 at 14:35
Daniel StandageDaniel Standage
2,555331
$endgroup$
add a comment |
$begingroup$
Most GFF parsers handle the work of reading annotation data into objects for convenient data access, but most do not handle the important task of resolving relationships between features. The tag Python library does both, grouping related features together for inspection, traversal, and feature-by-feature processing.
CAVEAT: The tag library only supports GFF3.
DISCLAIMER: I'm the developer of the tag library, so this is a shameless plug. :-)
answered Dec 13 '18 at 14:35
Daniel StandageDaniel Standage
2,555331
$endgroup$
add a comment |
$begingroup$
Most GFF parsers handle the work of reading annotation data into objects for convenient data access, but most do not handle the important task of resolving relationships between features. The tag Python library does both, grouping related features together for inspection, traversal, and feature-by-feature processing.
CAVEAT: The tag library only supports GFF3.
DISCLAIMER: I'm the developer of the tag library, so this is a shameless plug. :-)
answered Dec 13 '18 at 14:35
Daniel StandageDaniel Standage
2,555331
$endgroup$
Most GFF parsers handle the work of reading annotation data into objects for convenient data access, but most do not handle the important task of resolving relationships between features. The tag Python library does both, grouping related features together for inspection, traversal, and feature-by-feature processing.
CAVEAT: The tag library only supports GFF3.
DISCLAIMER: I'm the developer of the tag library, so this is a shameless plug. :-)
answered Dec 13 '18 at 14:35
Daniel StandageDaniel Standage
2,555331
answered Dec 13 '18 at 14:35
Daniel StandageDaniel Standage
2,555331
answered Dec 13 '18 at 14:35
Daniel StandageDaniel Standage
2,555331
answered Dec 13 '18 at 14:35
Daniel StandageDaniel Standage
2,555331
2,555331
add a comment |
add a comment |
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