Importing GFF file with Biopython

up vote
3
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?

asked 2 days ago

Alex Summers

161

New contributor

Please remember to confirm an answer once you've received one.
– Stephopolis
8 hours ago

add a comment |

up vote
3
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?

asked 2 days ago

Alex Summers

161

New contributor

Please remember to confirm an answer once you've received one.
– Stephopolis
8 hours ago

add a comment |

up vote
3
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?

asked 2 days ago

Alex Summers

161

New contributor

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

asked 2 days ago

Alex Summers

161

New contributor

asked 2 days ago

Alex Summers

161

New contributor

asked 2 days ago

Alex Summers

161

New contributor

asked 2 days ago

Alex Summers

161

asked 2 days ago

Alex Summers

161

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
8 hours ago

add a comment |

Please remember to confirm an answer once you've received one.
– Stephopolis
8 hours ago

Please remember to confirm an answer once you've received one.
– Stephopolis
8 hours ago

add a comment |

2 Answers
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up vote
7
down vote

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 2 days ago

conchoecia

1,287123

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 7 hours ago

Joe Healey

29516

add a comment |

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2 Answers
2

active

oldest

votes

2 Answers
2

active

oldest

votes

up vote
7
down vote

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 2 days ago

conchoecia

1,287123

add a comment |

up vote
7
down vote

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 2 days ago

conchoecia

1,287123

add a comment |

up vote
7
down vote

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 2 days ago

conchoecia

1,287123

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 2 days ago

conchoecia

1,287123

answered 2 days ago

conchoecia

1,287123

answered 2 days ago

conchoecia

1,287123

answered 2 days ago

conchoecia

1,287123

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.

answered 7 hours 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.

answered 7 hours 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.

answered 7 hours ago

Joe Healey

29516

I would use BCBio for gff handling as it is written to directly interface with BioPython’s object model.

answered 7 hours ago

Joe Healey

29516

answered 7 hours ago

Joe Healey

29516

answered 7 hours ago

Joe Healey

29516

answered 7 hours ago

Joe Healey

29516

add a comment |

Alex Summers is a new contributor. Be nice, and check out our Code of Conduct.

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