Package Bio :: Package Prosite :: Module Prodoc
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Module Bio.Prosite.Prodoc

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.
Classes
Dictionary Accesses a Prodoc file using a dictionary interface.
ExPASyDictionary Access PRODOC at ExPASy using a read-only dictionary interface.
Iterator Returns one record at a time from a Prodoc file.
Record Holds information from a Prodoc record.
RecordParser Parses Prodoc data into a Record object.
Reference Holds information from a Prodoc citation.
_RecordConsumer Consumer that converts a Prodoc record to a Record object.
_Scanner Scans Prodoc-formatted data.

Function Summary
  index_file(filename, indexname, rec2key)
index_file(filename, indexname, rec2key=None)
  _extract_record(handle)
_extract_record(handle) -> str

Function Details

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.

_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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