sugar._io.tab.blast module

BLAST reader for output generated with outfmt 7 (preferred), 6 or 10

sugar._io.tab.blast.is_fts_blast(f, outfmt=None, **kw)[source]
sugar._io.tab.blast.read_fts_blast(f, *, sep='\t', outfmt=None, ftype=None, comments=None)[source]

BLAST reader for output generated with option outfmt 7 (preferred), 6, or 10

Parameters:

  • sep (str) – Separator of fields, use ',' for outfmt 10, default '\t', can be set to None for any whitespace.

  • outfmt (str) – The outfmt string passed to BLAST, can be omitted for outfmt 7 or default outfmt 6 or 10 output.

  • ftype (str) – Parameter used as ftype, if parameter is not present use the value of ftype itself.

  • comments (list) – comment lines inside the file are stored in the comments list (optional)

Warning

This function should NOT be called directly, it registers via read_fts(), call this instead.