Package Bio :: Package Motif :: Package Parsers :: Module AlignAce :: Class AlignAceScanner
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Class AlignAceScanner

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Scannner for AlignACE output

Methods: feed Feed data into the scanner.

The scanner generates (and calls the consumer) the following types of events:

noevent - blank line

version - AlignACE version number command_line - AlignACE command line string parameters - the begining of the parameters parameter - the line containing a parameter sequences - the begining of the sequences list sequence - line containing the name of the input sequence (and a respective number) motif - the begining of the motif (contains the number) motif_hit - one hit for a motif motif_mask - mask of the motif (space - gap, asterisk - significant position) motif_score - MAP score of the motif - approx. N * log R, where R == (num. of actual occur.) / (num. of occur. expected by random.)

Instance Methods [hide private]
 
feed(S, handle, consumer)
Feed in a AlignACE report for scanning.
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Method Details [hide private]

feed(S, handle, consumer)

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Feed in a AlignACE report for scanning. handle is a file-like object that contains the AlignACE report. consumer is a Consumer object that will receive events as the report is scanned.