Bio.SeqIO.UniprotIO module¶
Bio.SeqIO support for the “uniprot-xml” file format.
See Also: http://www.uniprot.org
The UniProt XML format essentially replaces the old plain text file format originally introduced by SwissProt (“swiss” format in Bio.SeqIO).
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Bio.SeqIO.UniprotIO.
UniprotIterator
(source, alphabet=None, return_raw_comments=False)¶ Iterate over UniProt XML as SeqRecord objects.
parses an XML entry at a time from any UniProt XML file returns a SeqRecord for each iteration
This generator can be used in Bio.SeqIO
Argument source is a file-like object or a path to a file.
Optional argument alphabet should not be used anymore.
return_raw_comments = True –> comment fields are returned as complete XML to allow further processing skip_parsing_errors = True –> if parsing errors are found, skip to next entry
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class
Bio.SeqIO.UniprotIO.
Parser
(elem, alphabet=None, return_raw_comments=False)¶ Bases:
object
Parse a UniProt XML entry to a SeqRecord.
Optional argument alphabet is no longer used.
return_raw_comments=True to get back the complete comment field in XML format
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__init__
(self, elem, alphabet=None, return_raw_comments=False)¶ Initialize the class.
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parse
(self)¶ Parse the input.
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