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.
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Record
Holds information from a SwissProt record.
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Reference
Holds information from 1 references in a SwissProt entry.
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Dictionary
Accesses a SwissProt file using a dictionary interface.
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RecordParser
Parses SwissProt data into a Record object.
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SequenceParser
Parses SwissProt data into a standard SeqRecord object.
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_Scanner
Scans SwissProt-formatted data.
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_RecordConsumer
Consumer that converts a SwissProt record to a Record object.
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_SequenceConsumer
Consumer that converts a SwissProt record to a SeqRecord object.
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_CHOMP = ' \n\r\t.,; '
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__package__ = ' Bio.SwissProt '
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__warningregistry__ = { ( ' Bio.SwissProt.SProt is deprecated. Pl ...
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xml_support = 1
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index_file(filename,
indexname,
rec2key=None)
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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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__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}
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