MakeDb assigning failed germlines to None

[Jason Vander Heiden]

MakeDb is assigning None to GERMLINE_IMGT when a failure during germline reconstruction occurs. This should be an empty string instead.

[Jason Vander Heiden]

May be specific to MakeDb-igblast.

First thing to check is that Receptor.ReceptorData.nucleotide (and Receptor.ReceptorData.aminoacid) properly converts None to an empty string when deparse=True. Changing the tuple from ('NA', 'None') to ('NA', 'None', None) may be sufficient (need to test).

[Kenneth Hoehn]

@javh I haven't been able to reproduce this in the example (S43) database. Any recommendations for data to reproduce this error?

[Jason Vander Heiden]

Change the values of one of the positional fields in the igblast file (reference start/end, etc). That should force it to fail.

[Kenneth Hoehn]

Got it to work for igblast based on your suggestion. Think that's sufficient testing or do we need to try it on other input formats?

[Jason Vander Heiden]

That should be sufficient.

[Kenneth Hoehn]

changed line 589 of Receptor.py to:

# Nucleotide sequence type conversion
@staticmethod
def nucleotide(v, deparse=False):
    if not deparse:
        try:
            #return '' if v in ('NA', 'None') else Seq(v, IUPAC.ambiguous_dna).upper()
            return '' if v in ('NA', 'None') else v.upper()
        except:
            return ''
    else:
        return '' if v in ('NA', 'None', None) else str(v)

[Kenneth Hoehn]

Also changed

    # Sequence type conversion
    @staticmethod
    def aminoacid(v, deparse=False):
        if not deparse:
            try:
                #return '' if v in ('NA', 'None') else Seq(v, IUPAC.extended_protein).upper()
                return '' if v in ('NA', 'None') else v.upper()
            except:
                return ''
        else:
            return '' if v in ('NA', 'None', None) else str(v)

[Kenneth Hoehn]

Both changes are in commit 3e7b3ef