Bio.ExPASy.ScanProsite module
Code for calling and parsing ScanProsite from ExPASy.
- class Bio.ExPASy.ScanProsite.Record
Bases:
list
Represents search results returned by ScanProsite.
This record is a list containing the search results returned by ScanProsite. The record also contains the data members n_match, n_seq, capped, and warning.
- __init__()
Initialize the class.
- Bio.ExPASy.ScanProsite.scan(seq='', mirror='https://prosite.expasy.org', output='xml', **keywords)
Execute a ScanProsite search.
- Arguments:
- mirror: The ScanProsite mirror to be used
(default: https://prosite.expasy.org).
- seq: The query sequence, or UniProtKB (Swiss-Prot,
TrEMBL) accession
- output: Format of the search results
(default: xml)
Further search parameters can be passed as keywords; see the documentation for programmatic access to ScanProsite at https://prosite.expasy.org/scanprosite/scanprosite_doc.html for a description of such parameters.
This function returns a handle to the search results returned by ScanProsite. Search results in the XML format can be parsed into a Python object, by using the Bio.ExPASy.ScanProsite.read function.
- Bio.ExPASy.ScanProsite.read(handle)
Parse search results returned by ScanProsite into a Python object.
- class Bio.ExPASy.ScanProsite.Parser
Bases:
ExpatParser
Process the result from a ScanProsite search (PRIVATE).
- __init__()
Initialize the class.
- feed(data, isFinal=0)
Raise an Error if plain text is received in the data.
This is to show the Error messages returned by ScanProsite.
- class Bio.ExPASy.ScanProsite.ContentHandler
Bases:
ContentHandler
Process and fill in the records, results of the search (PRIVATE).
- integers = ('start', 'stop')
- strings = ('sequence_ac', 'sequence_id', 'sequence_db', 'signature_ac', 'level', 'level_tag')
- __init__()
Initialize the class.
- startElement(name, attrs)
Define the beginning of a record and stores the search record.
- endElement(name)
Define the end of the search record.
- characters(content)
Store the record content.