Answers.Body: <p>I would use <code>BCBio</code> for gff handling as it is written to directly interface with BioPython’s object model.</p>
  
  <p>The only downside is that I believe it is no longer actively supported. It is however the package that the <a href="https://biopython.org/wiki/GFF_Parsing" rel="nofollow noreferrer">BioPython docs</a> 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.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-12-11T19:53:27.250Z
Answers.LastActivityDate: 2018-12-11T19:53:27.250Z
Answers.UserDisplayName: Joe Healey
Answers.Body: <p>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 <a href="https://tag.readthedocs.io/en/stable/" rel="nofollow noreferrer"><strong>tag</strong> Python library</a> does both, grouping related features together for inspection, traversal, and feature-by-feature processing.</p>
  
  <p><strong>CAVEAT</strong>: The tag library only supports GFF3.</p>
  
  <p><strong>DISCLAIMER</strong>: I'm the developer of the tag library, so this is a shameless plug. :-)</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-12-13T14:35:19.103Z
Answers.LastActivityDate: 2018-12-13T14:35:19.103Z
Answers.UserDisplayName: Daniel Standage
Answers.Body: <p>No, <a href="https://biopython.org/wiki/GFF_Parsing" rel="noreferrer">there is currently no GFF support in biopython</a>. </p>
  
  <p><a href="https://github.com/daler/gffutils" rel="noreferrer">However, you can read in GFF files into python using this package, gffutils</a>. There are also a few other packages to read/write GFF files, like <a href="https://pypi.org/project/gff3/" rel="noreferrer"><code>gff3</code></a>.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-12-10T02:57:42.623Z
Answers.LastActivityDate: 2018-12-10T02:57:42.623Z
Answers.UserDisplayName: conchoecia
Body: <p>Is there a way to import a GFF file for an organism with Biopython in the same way you can for a Genbank file?</p>
  
  <p>For example,</p>
  
  <pre><code>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)
  </code></pre>
  
  <p>This will import a Gebank xml file for Pseudomonas putida.  Is there a way to do this for a GFF file?</p>
  
Tags: <python><phylogenetics><genbank><gff>
Title: Importing GFF file with Biopython
ThreadText: # Importing GFF file with Biopython
  
  (Asked by: username_0 on 2018-12-10)
  
  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?
  
  **Tags:** python, phylogenetics, genbank, gff
  
  
  ---
  
  ## 3 answers
  
  ### Answer by username_3 on 2018-12-10. Score: 10 | Accepted answer
  
  No, [there is currently no GFF support in biopython](https://biopython.org/wiki/GFF_Parsing).
  
  [However, you can read in GFF files into python using this package, gffutils](https://github.com/daler/gffutils). There are also a few other packages to read/write GFF files, like [`gff3`](https://pypi.org/project/gff3/).
  
  
  ---
  
  ### Answer by username_1 on 2018-12-11. Score: 2
  
  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](https://biopython.org/wiki/GFF_Parsing) 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.
  
  
  ---
  
  ### Answer by username_2 on 2018-12-13. Score: 1
  
  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](https://tag.readthedocs.io/en/stable/) 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. :-)
  
  
  ---
  
  