Package Bio :: Package SeqIO :: Module SwissIO
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Module SwissIO

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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).
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_make_seqfeature(name, from_res, to_res, description, ft_id)
Construct SeqFeature from feature data from parser (PRIVATE).
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SwissIterator(handle)
Breaks up a Swiss-Prot/UniProt file into SeqRecord objects.
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Variables [hide private]
  __package__ = 'Bio.SeqIO'
Function Details [hide private]

_make_position(location_string, offset=0)

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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)

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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.