biopython

v1.71.0

biopython v1.71.0 Bio.AlignIO.StockholmIO.StockholmIterator

Loads a Stockholm file from PFAM into MultipleSeqAlignment objects.

The file may contain multiple concatenated alignments, which are loaded and returned incrementally.

This parser will detect if the Stockholm file follows the PFAM conventions for sequence specific meta-data (lines starting and

Any annotation which does not follow the PFAM conventions is currently ignored.

If an accession is provided for an entry in the meta data, IT WILL NOT be used as the record.id (it will be recorded in the record’s annotations). This is because some files have (sub) sequences from different parts of the same accession (differentiated by different start-end positions).

Wrap-around alignments are not supported - each sequences must be on a single line. However, interlaced sequences should work.

For more information on the file format, please see: http://sonnhammer.sbc.su.se/Stockholm.html https://en.wikipedia.org/wiki/Stockholm_format http://bioperl.org/formats/alignment_formats/Stockholm_multiple_alignment_format.html

For consistency with BioPerl and EMBOSS we call this the “stockholm” format.

Link to this section Summary

Functions

__next__()

Parse the next alignment from the handle

_get_meta_data()

Take an itentifier and returns dict of all meta-data matching it

_identifier_split()

Return (name, start, end) string tuple from an identier

_populate_meta_data()

Add meta-date to a SecRecord’s annotations dictionary

Link to this section Functions

Link to this function __next__()

Parse the next alignment from the handle.

Link to this function _get_meta_data()

Take an itentifier and returns dict of all meta-data matching it.

For example, given “Q9PN73_CAMJE/149-220” will return all matches to this or “Q9PN73_CAMJE” which the identifier without its /start-end suffix.

In the example below, the suffix is required to match the AC, but must be removed to match the OS and OC meta-data::

...
Q9PN73_CAMJE/149-220               NKA...
...

This function will return an empty dictionary if no data is found.

Link to this function _identifier_split()

Return (name, start, end) string tuple from an identier.

Link to this function _populate_meta_data()

Add meta-date to a SecRecord’s annotations dictionary.

This function applies the PFAM conventions.