select_uniprot_variants cannot handle mismatches with canonical transcript for a given UniProt

[stuartmac]

from variants.to_table import select_uniprot_variants
select_uniprot_variants('P11586')
2016-02-08 09:36:41,670 - INFO - Starting new HTTP connection (1): www.uniprot.org 
2016-02-08 09:36:41,994 - DEBUG - "GET /uniprot/P11586 HTTP/1.1" 200 None 
2016-02-08 09:36:42,336 - INFO - Starting new HTTP connection (1): www.uniprot.org 
2016-02-08 09:36:42,386 - DEBUG - "GET /uniprot/?query=accession%3AP11586&contact=&columns=organism%2Csequence&format=tab HTTP/1.1" 200 None 
2016-02-08 09:36:42,390 - INFO - Starting new HTTP connection (1): rest.ensembl.org 
2016-02-08 09:36:42,934 - DEBUG - "GET /xrefs/symbol/homo_sapiens/P11586 HTTP/1.1" 200 222 
2016-02-08 09:36:42,937 - INFO - Starting new HTTP connection (1): rest.ensembl.org 
2016-02-08 09:36:43,474 - DEBUG - "GET /sequence/id/ENSP00000450560?type=protein HTTP/1.1" 200 261 
2016-02-08 09:36:43,475 - WARNING - Sequences don't match! skipping... ENSP00000450560 
2016-02-08 09:36:43,477 - INFO - Starting new HTTP connection (1): rest.ensembl.org 
2016-02-08 09:36:44,083 - DEBUG - "GET /sequence/id/ENSP00000216605?type=protein HTTP/1.1" 200 935 
2016-02-08 09:36:44,084 - WARNING - Sequences don't match! skipping... ENSP00000216605 
Traceback (most recent call last):
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2883, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-13-974825407562>", line 1, in <module>
    select_uniprot_variants('P11586')
  File "/Users/smacgowan/PycharmProjects/ProteoFAV/variants/to_table.py", line 444, in select_uniprot_variants
    table = pd.concat(tables)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pandas/tools/merge.py", line 812, in concat
    copy=copy)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pandas/tools/merge.py", line 845, in __init__
    raise ValueError('No objects to concatenate')
ValueError: No objects to concatenate

This happened because there was a mismatch between the EnsEMBL and UniProt sequences:

We can work around it by attempting a 'permissive' EnsEMBL - UniProt comparison that just checks that the sequences are of the same length and log the number of mismatches.

[biomadeira]

@stuartmac we have a method compare_uniprot_ensembl_sequence that would do this, but doesn't log the number of mismatches yet

[stuartmac]

@biomadeira I implemented one yesterday on my branch ca1bdd4

[stuartmac]

@biomadeira @tbrittoborges That's interesting, the fix was pulled into master even though I opened the pull request before I made that change. So the branch is pulled in its state at the time of the merge and not at the time of the pull request (?).

[tbrittoborges]

I accepted the PR yesterday.