Class BlastErrorParser
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ParserSupport.AbstractParser --+
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BlastErrorParser
Attempt to catch and diagnose BLAST errors while parsing.
This utilizes the BlastParser module but adds an additional layer of
complexity on top of it by attempting to diagnose ValueErrors that may
actually indicate problems during BLAST parsing.
Current BLAST problems this detects are: o LowQualityBlastError - When
BLASTing really low quality sequences (ie. some GenBank entries which are
just short streches of a single nucleotide), BLAST will report an error
with the sequence and be unable to search with this. This will lead to a
badly formatted BLAST report that the parsers choke on. The parser will
convert the ValueError to a LowQualityBlastError and attempt to provide
useful information.
__init__(self,
bad_report_handle=None)
(Constructor)
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Initialize a parser that tries to catch BlastErrors.
Arguments: o bad_report_handle - An optional argument specifying a
handle where bad reports should be sent. This would allow you to save all
of the bad reports to a file, for instance. If no handle is specified,
the bad reports will not be saved.
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Attempt to diagnose an error in the passed handle.
Arguments: o handle - The handle potentially containing the error o
data_record - The data record partially created by the consumer.
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