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.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: Bio.Align.interfaces.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.

__init__(source)

Create an AlignmentIterator object.

Arguments:

• source - input data or file name

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({})