Module SwissIO
source code
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.
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_make_position(location_string,
offset=0)
Turn a Swiss location position into a SeqFeature position object
(PRIVATE). |
source code
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_make_seqfeature(name,
from_res,
to_res,
description,
ft_id)
Construct SeqFeature from feature data from parser (PRIVATE). |
source code
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__package__ = ' Bio.SeqIO '
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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.
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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.
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