Package Biskit :: Package Mod :: Module NCBIStandalone :: Class BlastErrorParser

Class 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 SyntaxError's 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 SyntaxError to a LowQualityBlastError and attempt to provide useful information.

Instance Methods

[show private]

__init__(self, bad_report_handle=None)
Initialize a parser that tries to catch BlastErrors.

parse(self, handle)
Parse a handle, attempting to diagnose errors.

_diagnose_error(self, handle, data_record)
Attempt to diagnose an error in the passed handle.

Inherited from Bio.ParserSupport.AbstractParser: parse_file, parse_str

Method Details

[show private]

init(self, bad_report_handle=None)
(Constructor)

source code

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.

parse(self, handle)

source code

Parse a handle, attempting to diagnose errors.

Overrides: Bio.ParserSupport.AbstractParser.parse

Class BlastErrorParser

__init__(self, bad_report_handle=None) (Constructor)

parse(self, handle)

_diagnose_error(self, handle, data_record)

init(self, bad_report_handle=None)
(Constructor)