[Biopython-dev] [Biopython (old issues only) - Bug #3156] (Closed) UniProt XML and SwissProt parsers silently fail to parse all of database references

[redmine at redmine.open-bio.org]

Issue #3156 has been updated by Vincent Davis.

Description updated
Status changed from New to Closed
Assignee changed from Biopython Dev Mailing List to Vincent Davis
% Done changed from 0 to 100

working as designed/intended. Closing

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Bug #3156: UniProt XML and SwissProt parsers silently fail to parse all of database references
https://redmine.open-bio.org/issues/3156#change-15358

* Author: Renato Alves
* Status: Closed
* Priority: Normal
* Assignee: Vincent Davis
* Category: Main Distribution
* Target version: Not Applicable
* URL: 
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Example code:

from Bio import SeqIO, ExPASy
entry = SeqIO.read(ExPASy.get_sprot_raw('P31946'), 'swiss')

If you then inspect entry.dbxrefs, you can see that it includes:

['Ensembl:ENST00000353703', 'Ensembl:ENST00000372839']

but not
['Ensembl:ENSP00000300161', 'Ensembl:ENSG00000166913'. 'Ensembl:ENSP00000361930', 'Ensembl:ENSG00000166913']

which are present in the original file as:
DR   Ensembl; ENST00000353703; ENSP00000300161; ENSG00000166913.
DR   Ensembl; ENST00000372839; ENSP00000361930; ENSG00000166913.


The same happens with the XML format and the new uniprot-xml parser where the original file contains:

<dbReference type="Ensembl" id="ENST00000353703" key="75">
<property type="protein sequence ID" value="ENSP00000300161" />
<property type="gene ID" value="ENSG00000166913" />
</dbReference>



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