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

source code

This module is OBSOLETE. Most of the functionality in this module has moved to Bio.ExPASy.Prodoc; please see

Bio.ExPASy.Prodoc.read To read a Prodoc file containing one entry. Bio.ExPASy.Prodoc.parse Iterates over entries in a Prodoc file. Bio.ExPASy.Prodoc.Record Holds Prodoc data. Bio.ExPASy.Prodoc.Reference Holds data from a Prodoc reference.

The other functions and classes in Bio.Prosite.Prodoc (including Bio.Prosite.Prodoc.index_file and Bio.Prosite.Prodoc.Dictionary) are considered deprecated, and were not moved to Bio.ExPASy.Prodoc. If you use this functionality, please contact the Biopython developers at biopython-dev@biopython.org to avoid permanent removal of this module from Biopython.

This module provides code to work with the prosite.doc file from Prosite, available at http://www.expasy.ch/prosite/.

Tested with: Release 15.0, July 1998 Release 16.0, July 1999 Release 20.22, 13 November 2007

Functions: parse Iterates over entries in a Prodoc file. index_file Index a Prodoc file for a Dictionary. _extract_record Extract Prodoc data from a web page.

Classes: Record Holds Prodoc data. Reference Holds data from a Prodoc reference. Dictionary Accesses a Prodoc file using a dictionary interface. RecordParser Parses a Prodoc record into a Record object.

_Scanner Scans Prodoc-formatted data. _RecordConsumer Consumes Prodoc data to a Record object.

Classes [hide private]
  Record
Holds information from a Prodoc record.
  Reference
Holds information from a Prodoc citation.
  Dictionary
Accesses a Prodoc file using a dictionary interface.
  RecordParser
Parses Prodoc data into a Record object.
  _Scanner
Scans Prodoc-formatted data.
  _RecordConsumer
Consumer that converts a Prodoc record to a Record object.
Functions [hide private]
 
parse(handle) source code
 
read(handle) source code
 
index_file(filename, indexname, rec2key=None)
Index a Prodoc file.
source code
Variables [hide private]
  __package__ = 'Bio.Prosite'
  xml_support = 1
Function Details [hide private]

index_file(filename, indexname, rec2key=None)

source code 

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.