Package Bio :: Package SeqIO :: Module SwissIO

Module 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.

Functions

[hide private]

_make_position(location_string, offset=0)
Turn a Swiss location position into a SeqFeature position object (PRIVATE).

source code

_make_seqfeature(name, from_res, to_res, description, ft_id)
Construct SeqFeature from feature data from parser (PRIVATE).

source code

SwissIterator(handle)
Breaks up a Swiss-Prot/UniProt file into SeqRecord objects.

source code

Function Details

[hide private]

_make_position(location_string, offset=0)

source code

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.

SwissIterator(handle)

source code

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.