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SProt.py
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 Seq 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.
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Imported modules
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from Bio import File, Index, Alphabet, Seq, SeqRecord
from Bio.ParserSupport import *
from Bio.WWW import ExPASy, RequestLimiter
import os
import string
from types import *
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Functions
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index_file
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index_file
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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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Exceptions
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KeyError, "duplicate key %s found" % key
KeyError, "empty sequence key was produced"
ValueError, "%s does not exist" % filename
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Classes
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| Dictionary |
Accesses a SwissProt file using a dictionary interface.
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| ExPASyDictionary |
Access SwissProt at ExPASy using a read-only dictionary interface.
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| Iterator |
Returns one record at a time from a SwissProt file.
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| Record |
Holds information from a SwissProt record.
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| RecordParser |
Parses SwissProt data into a Record object.
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| Reference |
Holds information from 1 references in a SwissProt entry.
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| SequenceParser |
Parses SwissProt data into a Seq object.
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| _RecordConsumer |
Consumer that converts a SwissProt record to a Record object.
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| _Scanner |
Scans SwissProt-formatted data.
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| _SequenceConsumer |
Consumer that converts a SwissProt record to a Seq object.
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