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

This module provides code to work with the sprotXX.dat file from SwissProt. http://www.expasy.ch/sprot/sprot-top.html

Tested with: Release 37, Release 38, Release 39

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. ExPASyDictionary Accesses SwissProt records from ExPASy. 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 Record object. _SequenceConsumer Consumes SwissProt data to a Seq object.

Functions: index_file Index a SwissProt file for a Dictionary.
Classes
Dictionary Accesses a SwissProt file using a dictionary interface.
ExPASyDictionary Access SwissProt at ExPASy using a read-only dictionary interface.
Iterator Returns one record at a time from a SwissProt file.
Record Holds information from a SwissProt record.
RecordParser Parses SwissProt data into a Record object.
Reference Holds information from 1 references in a SwissProt entry.
SequenceParser Parses SwissProt data into a standard SeqRecord object.

Function Summary
  index_file(filename, indexname, rec2key)
index_file(filename, indexname, rec2key=None)

Function Details

index_file(filename, indexname, rec2key=None)

index_file(filename, indexname, rec2key=None)

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.

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