biopython

v1.71.0

biopython v1.71.0 Bio.SeqIO.SwissIO

Bio.SeqIO support for the “swiss” (aka SwissProt/UniProt) file format.

You are expected to use this module via the Bio.SeqIO functions. See also the Bio.SwissProt module which offers more than just accessing the sequences as SeqRecord objects.

See also Bio.SeqIO.UniprotIO.py which supports the “uniprot-xml” format.

Link to this section Summary

Functions

SwissIterator()

Breaks up a Swiss-Prot/UniProt file into SeqRecord objects

_make_position()

Turn a Swiss location position into a SeqFeature position object (PRIVATE)

_make_seqfeature()

Construct SeqFeature from feature data from parser (PRIVATE)

Link to this section Functions

Link to this function SwissIterator()

Breaks up a Swiss-Prot/UniProt file into SeqRecord objects.

Every section from the ID line to the terminating // becomes a single SeqRecord with associated annotation and features.

This parser is for the flat file “swiss” format as used by:

  • Swiss-Prot aka SwissProt
  • TrEMBL
  • UniProtKB aka UniProt Knowledgebase

For consistency with BioPerl and EMBOSS we call this the “swiss” format. See also the SeqIO support for “uniprot-xml” format.

Rather than calling it directly, you are expected to use this parser via Bio.SeqIO.parse(…, format=”swiss”) instead.

Link to this function _make_position()

Turn a Swiss location position into a SeqFeature position object (PRIVATE).

An offset of -1 is used with a start location to make it pythonic.

Link to this function _make_seqfeature()

Construct SeqFeature from feature data from parser (PRIVATE).