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c_to_p doesn't support inv #501

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icebert opened this issue Jul 22, 2018 · 0 comments
Closed

c_to_p doesn't support inv #501

icebert opened this issue Jul 22, 2018 · 0 comments

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@icebert
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icebert commented Jul 22, 2018

>>> import hgvs.parser
>>> import hgvs.dataproviders.uta
>>> import hgvs.assemblymapper
>>>
>>> hp = hgvs.parser.Parser()
>>> hdp = hgvs.dataproviders.uta.connect()
>>> am = hgvs.assemblymapper.AssemblyMapper(hdp)
>>>
>>> var_c = hp.parse_hgvs_variant('NM_001637.3:c.1582_1583inv')
>>> am.c_to_p(var_c)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/wm/Library/Python/2.7/lib/python/site-packages/hgvs/assemblymapper.py", line 117, in c_to_p
    var_out = super(AssemblyMapper, self).c_to_p(var_c)
  File "/Users/wm/Library/Python/2.7/lib/python/site-packages/hgvs/variantmapper.py", line 354, in c_to_p
    all_alt_data = builder.build_altseq()
  File "/Users/wm/Library/Python/2.7/lib/python/site-packages/hgvs/utils/altseqbuilder.py", line 150, in build_altseq
    raise NotImplementedError("c to p translation unsupported for {} type {}".format(self._var_c, edit_type))
NotImplementedError: c to p translation unsupported for NM_001637.3:c.1582_1583inv type <class 'hgvs.edit.Inv'>
reece pushed a commit that referenced this issue Jul 22, 2018
* Add support of inv for altseqbuilder

* Add tests of c_to_p for inv
reece pushed a commit that referenced this issue Aug 9, 2018
* Add support of inv for altseqbuilder

* Add tests of c_to_p for inv
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