Bio.SeqIO.SwissIO module

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.

Bio.SeqIO.SwissIO.SwissIterator(handle)

Break 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.