- Aug 10, 2015
- Aug 06, 2015
- Aug 04, 2015
- Jul 21, 2015
- Jul 20, 2015
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Vermaat authored
For transcripts without any UTR and CDS entries in the NCBI Mapview file (seems to happen for predicted genes), we generate one exon spanning the entire transcript.
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- Jul 16, 2015
- Jul 15, 2015
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Vermaat authored
Fix incorrect coloring of protein sequence positions
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Vermaat authored
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Vermaat authored
Use the Flask auto reloader in the debug server
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Vermaat authored
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Vermaat authored
Uncertain stop codon in protein descriptions (fs and ext)
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Vermaat authored
When a variant results in a frame shift or extension and we don't see a new stop codon in the RNA, the protein description should use the notation for an uncertain stop codon, e.g., `p.(Gln730Profs*?)` instead of `p.(Gln730Profs*96)` where 96 is just the last codon in our transcript [1]. To detect this, we now use `to_stop=False` in our `.translate()` calls, since that will explicitely return `*` characters for stop codons. We also slightly fix the coloring of changes in the protein sequence where previously changed stop codon characters where not included. [1] http://www.hgvs.org/mutnomen/FAQ.html#nostop
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- Jul 09, 2015
- Jul 03, 2015