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:
LowQualityBlastError     Except that indicates low quality query sequences.
BlastParser              Parses output from blast.
BlastErrorParser         Parses output and tries to diagnose possible errors.
PSIBlastParser           Parses output from psi-blast.
Iterator                 Iterates over a file of blast results.

_Scanner                 Scans output from standalone BLAST.
_BlastConsumer           Consumes output from blast.
_PSIBlastConsumer        Consumes output from psi-blast.
_HeaderConsumer          Consumes header information.
_DescriptionConsumer     Consumes description information.
_AlignmentConsumer       Consumes alignment information.
_HSPConsumer             Consumes hsp information.
_DatabaseReportConsumer  Consumes database report information.
_ParametersConsumer      Consumes parameters information.

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'>,
  48): True}