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variantmapper raises undefined exception #390

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reece opened this issue Dec 12, 2016 · 1 comment

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commented Dec 12, 2016

Originally reported by: Reece Hart (Bitbucket: reece, GitHub: reece)


Reported by @vfusaro:

In [1]: evm.c_to_g(hp.parse_hgvs_variant("NM_002186.2:c.1316A>G"))
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
/home/reece/projects/biocommons/hgvs/hgvs/shell.pyc in <module>()
----> 1 evm.c_to_g(hp.parse_hgvs_variant("NM_002186.2:c.1316A>G"))

/home/reece/projects/biocommons/hgvs/hgvs/variantmapper.pyc in c_to_g(self, var_c)
    420 
    421     def c_to_g(self, var_c):
--> 422         alt_ac = self._alt_ac_for_tx_ac(var_c.ac)
    423         var_out = super(EasyVariantMapper, self).c_to_g(var_c, alt_ac, alt_aln_method=self.alt_aln_method)
    424         if self.replace_reference:

/home/reece/projects/biocommons/hgvs/hgvs/variantmapper.pyc in _alt_ac_for_tx_ac(self, tx_ac)
    466                    if e['alt_aln_method'] == self.alt_aln_method and e['alt_ac'] in self.primary_assembly_accessions]
    467         if len(alt_acs) > 1:
--> 468             raise HGVSError("Multiple chromosomal alignments for {tx_ac} in {pa}"
    469                             "using {am} (likely paralog or pseudoautosomal region)".format(
    470                                 tx_ac=tx_ac,

NameError: global name 'HGVSError' is not defined

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commented Dec 12, 2016

Original comment by Reece Hart (Bitbucket: reece, GitHub: reece):


closes #390: fix missing HGVSError import in variantmapper

@reece reece added this to the 0.4.x milestone Mar 9, 2017
@reece reece closed this Mar 9, 2017
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