Package Bio :: Package MEME :: Module Parser :: Class MASTParser
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Class MASTParser

source code

ParserSupport.AbstractParser --+
                               |
                              MASTParser


Parser for MAST text output (OBSOLETE).
HTML output cannot be parsed, yet. Returns a MASTRecord

A MASTParser takes a file handle for a MAST text output file and 
returns a MASTRecord, containing the hits between motifs and 
sequences. The parser does some unusual line buffering to parse out 
match diagrams. Really complex diagrams often lead to an error message 
and p-values not being parsed for a given line.

Methods:
parse (handle): parses the data from the file handle passed to it.

Example:

f = open("mast_file.txt")
parser = MASTParser()
mast_record = parser.parse(f)
for motif in mast_record.motifs:
    for instance in motif.instances:
        print instance.motif_name, instance.sequence_name, instance.strand, instance.pvalue

This class is OBSOLETE; its functionality is now available through
Bio.Motif.Parsers.MAST.

Instance Methods [hide private]
 
__init__(self) source code
 
parse(self, handle) source code

Inherited from ParserSupport.AbstractParser: parse_file, parse_str

Method Details [hide private]

parse(self, handle)

source code 
Overrides: ParserSupport.AbstractParser.parse