sugar._io.tab.mmseqs module

MMseqs2 reader for output generated with option fmtmode 4 (preferred) or 0

sugar._io.tab.mmseqs.is_fts_mmseqs(f, *, sep='\t', outfmt=None, **kw)[source]
sugar._io.tab.mmseqs.read_fts_mmseqs(f, *, sep='\t', outfmt=None, ftype=None, comments=None)[source]

Tabular data reader for feature output generated by MMseqs2

Parameters:

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

  • outfmt (str) – The string passed to MMseqs2 option --format-output, can be omitted if MMseqs2 was called with --fmtmode 4 or --fmtmode 0 with default format-output

  • ftype (str) – Parameter used as ftype

  • 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.