Package Bio :: Package SwissProt :: Module SProt
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Module SProt

source code

This module provides code to work with the sprotXX.dat file from Utilities for working with FASTA-formatted sequences (DEPRECATED). http://www.expasy.ch/sprot/sprot-top.html

Please see Bio.SwissProt for alternatives for the functionality in this module.

Tested with: Release 37, Release 38, Release 39

Limited testing with: Release 51, 54

Classes: Record Holds SwissProt data. Reference Holds reference data from a SwissProt entry. Iterator Iterates over entries in a SwissProt file. Dictionary Accesses a SwissProt file using a dictionary interface. RecordParser Parses a SwissProt record into a Record object. SequenceParser Parses a SwissProt record into a SeqRecord object.

_Scanner Scans SwissProt-formatted data. _RecordConsumer Consumes SwissProt data to a SProt.Record object. _SequenceConsumer Consumes SwissProt data to a SeqRecord object.

Functions: index_file Index a SwissProt file for a Dictionary.

Classes [hide private]
  Record
Holds information from a SwissProt record.
  Reference
Holds information from 1 references in a SwissProt entry.
  Dictionary
Accesses a SwissProt file using a dictionary interface.
  RecordParser
Parses SwissProt data into a Record object.
  SequenceParser
Parses SwissProt data into a standard SeqRecord object.
  _Scanner
Scans SwissProt-formatted data.
  _RecordConsumer
Consumer that converts a SwissProt record to a Record object.
  _SequenceConsumer
Consumer that converts a SwissProt record to a SeqRecord object.
Functions [hide private]
 
parse(handle) source code
 
read(handle) source code
 
index_file(filename, indexname, rec2key=None)
Index a SwissProt file.
source code
Variables [hide private]
  _CHOMP = ' \n\r\t.,;'
  __package__ = 'Bio.SwissProt'
  __warningregistry__ = {('Bio.SwissProt.SProt is deprecated. Pl...
  xml_support = 1
Function Details [hide private]

index_file(filename, indexname, rec2key=None)

source code 

Index a SwissProt file. filename is the name of the file. indexname is the name of the dictionary. rec2key is an optional callback that takes a Record and generates a unique key (e.g. the accession number) for the record. If not specified, the entry name will be used.


Variables Details [hide private]

__warningregistry__

Value:
{('Bio.SwissProt.SProt is deprecated. Please use the functions Bio.Swi\
ssProt.parse or Bio.SwissProt.read if you want to get a SwissProt.Reco\
rd, or Bio.SeqIO.parse or Bio.SeqIO.read if you want to get a SeqRecor\
d. If these solutions do not work for you, please get in contact with \
the Biopython developers (biopython-dev@biopython.org).',
  <type 'exceptions.DeprecationWarning'>,
  39): True}