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 |
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Pattern
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Prodoc : This module provides code to work with the prosite.doc file from
Prosite.
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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. |
_RecordConsumer |
Consumer that converts a Prosite record to a Record object. |
_Scanner |
Scans Prosite-formatted data. |
Function Summary |
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index_file (filename,
indexname,
rec2key)
index_file(filename, indexname, rec2key=None) |
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scan_sequence_expasy (seq,
id,
exclude_frequent)
scan_sequence_expasy(seq=None, id=None, exclude_frequent=None) ->
list of PatternHit's |
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_extract_pattern_hits (handle)
_extract_pattern_hits(handle) -> list of PatternHit's |
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_extract_record (handle)
_extract_record(handle) -> str |
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.
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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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_extract_pattern_hits(handle)
_extract_pattern_hits(handle) -> list of PatternHit's
Extract hits from a web page. Raises a ValueError if there was an
error in the query.
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_extract_record(handle)
_extract_record(handle) -> str
Extract PROSITE data from a web page. Raises a ValueError if no data
was found in the web page.
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