Importing GFF file with Biopython
up vote
4
down vote
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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 12 hours ago
Daniel Standage
1,866324
asked Dec 10 at 2:19
Alex Summers
233
New contributor
Alex Summers is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
add a comment |
up vote
4
down vote
favorite
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 12 hours ago
Daniel Standage
1,866324
asked Dec 10 at 2:19
Alex Summers
233
New contributor
Alex Summers is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
Please remember to confirm an answer once you've received one.
– Stephopolis
2 days ago
add a comment |
up vote
4
down vote
favorite
up vote
4
down vote
favorite
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 12 hours ago
Daniel Standage
1,866324
asked Dec 10 at 2:19
Alex Summers
233
New contributor
Alex Summers is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
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 12 hours ago
Daniel Standage
1,866324
asked Dec 10 at 2:19
Alex Summers
233
New contributor
Alex Summers is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
edited 12 hours ago
Daniel Standage
1,866324
asked Dec 10 at 2:19
Alex Summers
233
New contributor
Alex Summers is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
edited 12 hours ago
Daniel Standage
1,866324
edited 12 hours ago
Daniel Standage
1,866324
edited 12 hours ago
Daniel Standage
1,866324
1,866324
asked Dec 10 at 2:19
Alex Summers
233
New contributor
Alex Summers is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
asked Dec 10 at 2:19
Alex Summers
233
asked Dec 10 at 2:19
Alex Summers
233
233
New contributor
Alex Summers is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
New contributor
Alex Summers is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
Alex Summers is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
Please remember to confirm an answer once you've received one.
– Stephopolis
2 days ago
add a comment |
Please remember to confirm an answer once you've received one.
– Stephopolis
2 days ago
Please remember to confirm an answer once you've received one.
– Stephopolis
2 days ago
Please remember to confirm an answer once you've received one.
– Stephopolis
2 days ago
add a comment |
3 Answers
3
active
oldest
votes
up vote
9
down vote
accepted
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 at 2:57
conchoecia
1,397123
add a comment |
up vote
1
down vote
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 2 days ago
Joe Healey
29516
add a comment |
up vote
0
down vote
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 12 hours ago
Daniel Standage
1,866324
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
up vote
9
down vote
accepted
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 at 2:57
conchoecia
1,397123
add a comment |
up vote
9
down vote
accepted
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 at 2:57
conchoecia
1,397123
add a comment |
up vote
9
down vote
accepted
up vote
9
down vote
accepted
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 at 2:57
conchoecia
1,397123
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 at 2:57
conchoecia
1,397123
answered Dec 10 at 2:57
conchoecia
1,397123
answered Dec 10 at 2:57
conchoecia
1,397123
answered Dec 10 at 2:57
conchoecia
1,397123
1,397123
add a comment |
add a comment |
up vote
1
down vote
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 2 days ago
Joe Healey
29516
add a comment |
up vote
1
down vote
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 2 days ago
Joe Healey
29516
add a comment |
up vote
1
down vote
up vote
1
down vote
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 2 days ago
Joe Healey
29516
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 2 days ago
Joe Healey
29516
answered 2 days ago
Joe Healey
29516
answered 2 days ago
Joe Healey
29516
answered 2 days ago
Joe Healey
29516
29516
add a comment |
add a comment |
up vote
0
down vote
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 12 hours ago
Daniel Standage
1,866324
add a comment |
up vote
0
down vote
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 12 hours ago
Daniel Standage
1,866324
add a comment |
up vote
0
down vote
up vote
0
down vote
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 12 hours ago
Daniel Standage
1,866324
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 12 hours ago
Daniel Standage
1,866324
answered 12 hours ago
Daniel Standage
1,866324
answered 12 hours ago
Daniel Standage
1,866324
answered 12 hours ago
Daniel Standage
1,866324
1,866324
add a comment |
add a comment |
Alex Summers is a new contributor. Be nice, and check out our Code of Conduct.
Alex Summers is a new contributor. Be nice, and check out our Code of Conduct.
Alex Summers is a new contributor. Be nice, and check out our Code of Conduct.
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