Package Bio :: Package MEME :: Module Parser :: Class _MASTConsumer
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Class _MASTConsumer


Consumer that can receive events from _MASTScanner.

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.
Method Summary
  __init__(self)
  _add_diagram_from_buffer(self, dummy)
  _add_line_to_buffer(self, line)
  _add_match_diagram(self, line)
  _add_motif(self, line)
  _add_motif_match(self, line)
  _add_sequence_match_with_diagram(self, line)
  _blank_buffer(self, dummy)
  _collapse_buffer(self, dummy)
  _database(self, line)
  _parse_buffer(self, dummy)
Parses the line buffer to get e-values for each instance of a motif.
  _set_current_seq(self, line)
  _version(self, line)
  noevent(self, line)

Method Details

_parse_buffer(self, dummy)

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.

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