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running for KIR #135

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droe-nmdp opened this issue Jan 18, 2019 · 0 comments
Open

running for KIR #135

droe-nmdp opened this issue Jan 18, 2019 · 0 comments
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@droe-nmdp
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Is this the correct syntax for KIR?
docker run -it --rm -v $PWD:/opt nmdpbioinformatics/pygfe seq2gfe -f /opt/2DL4_test.txt -l KIR2DL4 -k
2dl4_test.txt

When I run it that way, I get
File "/usr/local/lib/python3.6/dist-packages/seqann/sequence_annotation.py", line 159, in annotate
annotation=annotation)
File "/usr/local/lib/python3.6/dist-packages/seqann/sequence_annotation.py", line 212, in ref_align
b)
File "/usr/local/lib/python3.6/dist-packages/seqann/sequence_annotation.py", line 428, in _refseqs
length += float(self.refdata.feature_lengths[locus][fr][0])

The KIR allele is really KIR2DL4*0010201.

Any suggestions?
@mmaiers-nmdp mmaiers-nmdp self-assigned this Apr 3, 2019
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@mmaiers-nmdp @droe-nmdp