Bio.Align.hhr module

Bio.Align support for hhr files generated by HHsearch or HHblits in HH-suite.

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

class Bio.Align.hhr.AlignmentIterator(source)

Bases: Bio.Align.interfaces.AlignmentIterator

Alignment iterator for hhr output files generated by HHsearch or HHblits.

HHsearch and HHblits are part of the HH-suite of programs for Hidden Markov Models. An output files in the hhr format contains multiple pairwise alignments for a single query sequence.

fmt: Optional[str] = 'hhr'

__len__()

Return the number of alignments.

The number of alignments is cached. If not yet calculated, the iterator is rewound to the beginning, and the number of alignments is calculated by iterating over the alignments. The iterator is then returned to its original position in the file.

__abstractmethods__ = frozenset({})

__annotations__ = {'fmt': 'Optional[str]'}