Package Prosite
source code
Module for working with Prosite files from ExPASy (OBSOLETE).
Most of the functionality in this module has moved to
Bio.ExPASy.Prosite; please see
Bio.ExPASy.Prosite.read To read a Prosite file containing one
entry. Bio.ExPASy.Prosite.parse Iterates over entries in a
Prosite file. Bio.ExPASy.Prosite.Record Holds Prosite data.
For scan_sequence_expasy Scan a sequence for occurrences of Prosite
patterns. _extract_pattern_hits Extract Prosite patterns from a web page.
PatternHit Holds data from a hit against a Prosite pattern.
please see the new module Bio.ExPASy.ScanProsite.
The other functions and classes in Bio.Prosite (including
Bio.Prosite.index_file and Bio.Prosite.Dictionary) are considered
deprecated, and were not moved to Bio.ExPASy.Prosite. 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 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
Functions: parse Iterates over entries in a Prosite
file. 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.
Classes: Record Holds Prosite data. PatternHit
Holds data from a hit against a Prosite pattern. Dictionary
Accesses a Prosite file using a dictionary interface. RecordParser
Parses a Prosite record into a Record object.
_Scanner Scans Prosite-formatted data. _RecordConsumer
Consumes Prosite data to a Record object.
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Record
Holds information from a Prosite record.
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PatternHit
Holds information from a hit against a Prosite pattern.
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Dictionary
Accesses a Prosite file using a dictionary interface.
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RecordParser
Parses Prosite data into a Record object.
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_Scanner
Scans Prosite-formatted data.
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_RecordConsumer
Consumer that converts a Prosite record to a Record object.
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list of PatternHit's
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list of PatternHit's
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__package__ = ' Bio.Prosite '
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xml_support = 1
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scan_sequence_expasy(seq=None,
id=None,
exclude_frequent=None)
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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.
- Returns: list of PatternHit's
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Extract hits from a web page. Raises a ValueError if there was an
error in the query.
- Returns: list of PatternHit's
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index_file(filename,
indexname,
rec2key=None)
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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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