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: 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: str | None = 'hhr'

__len__()

Return the number of alignments.

The .hhr file’s summary table lists one row per alignment; the _read_header(self, stream) method counts the rows while parsing the header and caches the count in self._length.

__abstractmethods__ = frozenset({})

__annotations__ = {'fmt': 'str | None'}