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Prodoc.py
This module provides code to work with the prosite.doc file from
Prosite.
http://www.expasy.ch/prosite/
Tested with:
Release 15.0, July 1998
Release 16.0, July 1999
Classes:
Record Holds Prodoc data.
Reference Holds data from a Prodoc reference.
Iterator Iterates over entries in a Prodoc file.
Dictionary Accesses a Prodoc file using a dictionary interface.
ExPASyDictionary Accesses Prodoc records from ExPASy.
RecordParser Parses a Prodoc record into a Record object.
_Scanner Scans Prodoc-formatted data.
_RecordConsumer Consumes Prodoc data to a Record object.
Functions:
index_file Index a Prodoc file for a Dictionary.
_extract_record Extract Prodoc data from a web page.
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Imported modules
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from Bio import File, Index
from Bio.ParserSupport import *
from Bio.WWW import ExPASy
import re
import sgmllib
import string
import time
from types import *
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Functions
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_extract_record
index_file
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_extract_record
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_extract_record ( handle )
_extract_record(handle) -> str
Extract PRODOC data from a web page. Raises a ValueError if no
data was found in the web page.
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Exceptions
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ValueError, "No data found in web page."
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index_file
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index_file (
filename,
indexname,
rec2key=None,
)
index_file(filename, indexname, rec2key=None)
Index a Prodoc 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 id name will be used.
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Exceptions
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KeyError, "duplicate key %s found" % key
KeyError, "empty key was produced"
ValueError, "%s does not exist" % filename
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Classes
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| Dictionary |
Accesses a Prodoc file using a dictionary interface.
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| ExPASyDictionary |
Access PRODOC at ExPASy using a read-only dictionary interface.
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| Iterator |
Returns one record at a time from a Prodoc file.
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| Record |
Holds information from a Prodoc record.
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| RecordParser |
Parses Prodoc data into a Record object.
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| Reference |
Holds information from a Prodoc citation.
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| _RecordConsumer |
Consumer that converts a Prodoc record to a Record object.
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| _Scanner |
Scans Prodoc-formatted data.
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