Package Bio :: Package SeqIO :: Module UniprotIO
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Module UniprotIO

source code

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).

Classes [hide private]
  Parser
Parse a UniProt XML entry to a SeqRecord.
Functions [hide private]
 
UniprotIterator(handle, alphabet=ProteinAlphabet(), return_raw_comments=False)
Generator function to parse UniProt XML as SeqRecord objects.
source code
Variables [hide private]
  NS = '{http://uniprot.org/uniprot}'
  REFERENCE_JOURNAL = '%(name)s %(volume)s:%(first)s-%(last)s(%(...
  __package__ = 'Bio.SeqIO'
Function Details [hide private]

UniprotIterator(handle, alphabet=ProteinAlphabet(), return_raw_comments=False)

source code 

Generator function to parse 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

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


Variables Details [hide private]

REFERENCE_JOURNAL

Value:
'%(name)s %(volume)s:%(first)s-%(last)s(%(pub_date)s)'