Package Bio :: Package Blast :: Module NCBIStandalone
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Module NCBIStandalone

source code

Code for calling standalone BLAST and parsing plain text output (DEPRECATED).

Rather than parsing the human readable plain text BLAST output (which seems to change with every update to BLAST), we and the NBCI recommend you parse the XML output instead. The plain text parser in this module still works at the time of writing, but is considered obsolete and updating it to cope with the latest versions of BLAST is not a priority for us.

This module also provides code to work with the "legacy" standalone version of NCBI BLAST, tools blastall, rpsblast and blastpgp via three helper functions of the same name. These functions are very limited for dealing with the output as files rather than handles, for which the wrappers in Bio.Blast.Applications are preferred. Furthermore, the NCBI themselves regard these command line tools as "legacy", and encourage using the new BLAST+ tools instead. Biopython has wrappers for these under Bio.Blast.Applications (see the tutorial).

Classes [hide private]
  LowQualityBlastError
Error caused by running a low quality sequence through BLAST.
  ShortQueryBlastError
Error caused by running a short query sequence through BLAST.
  _Scanner
Scan BLAST output from blastall or blastpgp.
  BlastParser
Parses BLAST data into a Record.Blast object.
  PSIBlastParser
Parses BLAST data into a Record.PSIBlast object.
  _HeaderConsumer
  _DescriptionConsumer
  _AlignmentConsumer
  _HSPConsumer
  _DatabaseReportConsumer
  _ParametersConsumer
  _BlastConsumer
  _PSIBlastConsumer
  Iterator
Iterates over a file of multiple BLAST results.
  _BlastErrorConsumer
  BlastErrorParser
Attempt to catch and diagnose BLAST errors while parsing.
Functions [hide private]
 
_re_search(regex, line, error_msg) source code
 
_get_cols(line, cols_to_get, ncols=None, expected={}) source code
 
_safe_int(str) source code
 
_safe_float(str) source code
Variables [hide private]
  __package__ = 'Bio.Blast'
  __warningregistry__ = {('This module has been deprecated. Cons...
Variables Details [hide private]

__warningregistry__

Value:
{('This module has been deprecated. Consider Bio.SearchIO for parsing \
BLAST output instead.',
  <class 'Bio.BiopythonDeprecationWarning'>,
  30): True}