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. |
_RecordConsumer |
Consumer that converts a SwissProt record to a Record object. |
_Scanner |
Scans SwissProt-formatted data. |
_SequenceConsumer |
Consumer that converts a SwissProt record to a SeqRecord object. |
Function Summary |
|
index_file (filename,
indexname,
rec2key)
index_file(filename, indexname, rec2key=None) |
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.
-
|