Bio.Align.exonerate module

Bio.Align support for Exonerate output format.

This module provides support for Exonerate outputs. Exonerate is a generic tool for pairwise sequence comparison that allows you to align sequences using several different models.

Bio.Align.exonerate was tested on the following Exonerate versions and models:

  • version: 2.2

  • models: - affine:local - cdna2genome - coding2coding - est2genome - genome2genome - ner - protein2dna - protein2genome - ungapped - ungapped:translated

Although model testing were not exhaustive, the parser should be able to cope with all Exonerate models. Please file a bug report if you stumble upon an unparsable file.

You are expected to use this module via the Bio.Align functions.

class Bio.Align.exonerate.AlignmentWriter(target, fmt='vulgar')

Bases: Bio.Align.interfaces.AlignmentWriter

Alignment file writer for the Exonerate cigar and vulgar file format.

fmt: Optional[str] = 'Exonerate'
__init__(target, fmt='vulgar')

Create an AlignmentWriter object.

Arguments:

  • target - output stream or file name

  • fmt - write alignments in the vulgar (Verbose Useful Labelled

    Gapped Alignment Report) format (fmt=”vulgar”) or in the cigar (Compact Idiosyncratic Gapped Alignment Report) format (fmt=”cigar”). Default value is ‘vulgar’.

write_header(stream, alignments)

Write the header.

Write the footer.

__abstractmethods__ = frozenset({})
__annotations__ = {'fmt': 'Optional[str]'}
class Bio.Align.exonerate.AlignmentIterator(source)

Bases: Bio.Align.interfaces.AlignmentIterator

Alignment iterator for the Exonerate text, cigar, and vulgar formats.

Each line in the file contains one pairwise alignment, which are loaded and returned incrementally. Alignment score information such as the number of matches and mismatches are stored as attributes of each alignment.

fmt: Optional[str] = 'Exonerate'
__abstractmethods__ = frozenset({})
__annotations__ = {'fmt': 'Optional[str]'}