Package Prosite
source code
Module for working with Prosite files from ExPASy (DEPRECATED).
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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__warningregistry__ = { ( ' Bio.Prosite is deprecated, and will b ...
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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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__warningregistry__
- Value:
{ ( ' Bio.Prosite is deprecated, and will be removed in a future release
of Biopython. Most of the functionality is now provided by Bio.ExPASy
.Prosite. If you want to continue to use Bio.Prosite, please get in
contact via the mailing lists to avoid its permanent removal from Bio
python. ' ,
<class 'Bio.BiopythonDeprecationWarning'>,
66) : True}
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