Questions tagged [parsing]

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Biopython - extracting query coverage from XML Blast output

I need to extract (or to calculate precisely) the query coverage from Blast output. I am using NCBIWWW.qblast to query Blast in XML format. Is it possible to know the query coverage parsing the XML ...
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GTF parser for Python

I found this GTF parser for Python. However, it does not work with Scallop's GTF file: ...
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VCF spec: is it possible to have other alleles in addition to the MISSING value ('.') in ALTS?

I'm writing a VCF parser, so I have to consider and handle all corner cases regardless of how contrived they may seem. The specification is a bit unclear about the MISSING value ('.') in the ALTS ...