Bio.Align.tabular module
Bio.Align support for tabular output from BLAST or FASTA.
This module contains a parser for tabular output from BLAST run with the ‘-outfmt 7’ argument, as well as tabular output from William Pearson’s FASTA alignment tools using the ‘-m 8CB’ or ‘-m 8CC’ arguments.
- class Bio.Align.tabular.State(value)
Bases:
Enum
Enumerate alignment states needed when parsing a BTOP string.
- MATCH = 1
- QUERY_GAP = 2
- TARGET_GAP = 3
- NONE = 4
- class Bio.Align.tabular.AlignmentIterator(source)
Bases:
AlignmentIterator
Alignment iterator for tabular output from BLAST or FASTA.
For reading (pairwise) alignments from tabular output generated by BLAST run with the ‘-outfmt 7’ argument, as well as tabular output generated by William Pearson’s FASTA alignment programs with the ‘-m 8CB’ or ‘-m 8CC’ output formats.
- fmt: str | None = 'Tabular'
- parse_btop(btop)
Parse a BTOP string and return alignment coordinates.
A BTOP (Blast trace-back operations) string is used by BLAST to describe a sequence alignment.
- parse_cigar(cigar)
Parse a CIGAR string and return alignment coordinates.
A CIGAR string, as defined by the SAM Sequence Alignment/Map format, describes a sequence alignment as a series of lengths and operation (alignment/insertion/deletion) codes.
- __abstractmethods__ = frozenset({})