Package Bio :: Package Motif :: Package Parsers :: Module MEME :: Class _MASTConsumer
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Class _MASTConsumer

source code

Consumer that can receive events from _MASTScanner (DEPRECATED).

A _MASTConsumer parses lines from a mast text output file. The motif match diagrams are parsed using line buffering. Each of the buffering functions have a dummy variable that is required for testing using the Bio.ParserSupport.TaggingConsumer. If this variable isn't there, the TaggingConsumer barfs. In the _MASTScanner, None is passed in the place of this variable.

This class is DEPRECATED; please use the read() function in the module Bio.Motif.Parsers.MAST instead.

Instance Methods [hide private]
 
__init__(self) source code
 
_version(self, line) source code
 
_database(self, line) source code
 
_add_motif(self, line) source code
 
_add_match_diagram(self, line) source code
 
_add_sequence_match_with_diagram(self, line) source code
 
_add_diagram_from_buffer(self, dummy) source code
 
_set_current_seq(self, line) source code
 
_add_line_to_buffer(self, line) source code
 
_parse_buffer(self, dummy)
Parses the line buffer to get e-values for each instance of a motif.
source code
 
_blank_buffer(self, dummy) source code
 
_collapse_buffer(self, dummy) source code
 
_add_motif_match(self, line) source code
 
noevent(self, line) source code
Method Details [hide private]

_parse_buffer(self, dummy)

source code 

Parses the line buffer to get e-values for each instance of a motif. This buffer parser is the most likely point of failure for the MASTParser.