Package Bio :: Package Prosite
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Package Bio.Prosite

This module provides code to work with the prosite dat file from Prosite. http://www.expasy.ch/prosite/

Tested with: Release 15.0, July 1998 Release 16.0, July 1999 Release 17.0, Dec 2001 Release 19.0, Mar 2006

Classes: Record Holds Prosite data. PatternHit Holds data from a hit against a Prosite pattern. Iterator Iterates over entries in a Prosite file. Dictionary Accesses a Prosite file using a dictionary interface. ExPASyDictionary Accesses Prosite records from ExPASy. RecordParser Parses a Prosite record into a Record object.

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

Functions: scan_sequence_expasy Scan a sequence for occurrences of Prosite patterns. index_file Index a Prosite file for a Dictionary. _extract_record Extract Prosite data from a web page. _extract_pattern_hits Extract Prosite patterns from a web page.
Submodules
  • Pattern
  • Prodoc: This module provides code to work with the prosite.doc file from Prosite.

Classes
Dictionary Accesses a Prosite file using a dictionary interface.
ExPASyDictionary Access PROSITE at ExPASy using a read-only dictionary interface.
Iterator Returns one record at a time from a Prosite file.
PatternHit Holds information from a hit against a Prosite pattern.
Record Holds information from a Prosite record.
RecordParser Parses Prosite data into a Record object.

Function Summary
  index_file(filename, indexname, rec2key)
index_file(filename, indexname, rec2key=None)
  scan_sequence_expasy(seq, id, exclude_frequent)
scan_sequence_expasy(seq=None, id=None, exclude_frequent=None) -> list of PatternHit's

Function Details

index_file(filename, indexname, rec2key=None)

index_file(filename, indexname, rec2key=None)

Index a Prosite 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.

scan_sequence_expasy(seq=None, id=None, exclude_frequent=None)

scan_sequence_expasy(seq=None, id=None, exclude_frequent=None) -> list of PatternHit's

Search a sequence for occurrences of Prosite patterns. You can specify either a sequence in seq or a SwissProt/trEMBL ID or accession in id. Only one of those should be given. If exclude_frequent is true, then the patterns with the high probability of occurring will be excluded.

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