Class NcbiblastformatterCommandline
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object --+
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Application.AbstractCommandline --+
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_NcbibaseblastCommandline --+
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NcbiblastformatterCommandline
Wrapper for the NCBI BLAST+ program blast_formatter.
With the release of BLAST 2.2.24+ (i.e. the BLAST suite rewritten in
C++ instead of C), the NCBI added the ASN.1 output format option to all
the search tools, and extended the blast_formatter to support this as
input.
The blast_formatter command allows you to convert the ASN.1 output
into the other output formats (XML, tabular, plain text, HTML).
>>> from Bio.Blast.Applications import NcbiblastformatterCommandline
>>> cline = NcbiblastformatterCommandline(archive="example.asn", outfmt=5, out="example.xml")
>>> cline
NcbiblastformatterCommandline(cmd='blast_formatter', out='example.xml', outfmt=5, archive='example.asn')
>>> print cline
blast_formatter -out example.xml -outfmt 5 -archive example.asn
You would typically run the command line with cline() or via the
Python subprocess module, as described in the Biopython tutorial.
Note that this wrapper is for the version of blast_formatter from
BLAST 2.2.24+ (or later) which is when the NCBI first announced the
inclusion this tool. There was actually an early version in BLAST 2.2.23+
(and possibly in older releases) but this did not have the -archive
option (instead -rid is a mandatory argument), and is not supported by
this wrapper.
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__init__(self,
cmd=' blast_formatter ' ,
**kwargs)
Create a new instance of a command line wrapper object. |
source code
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Inherited from Application.AbstractCommandline :
__call__ ,
__repr__ ,
__setattr__ ,
__str__ ,
set_parameter
Inherited from object :
__delattr__ ,
__format__ ,
__getattribute__ ,
__hash__ ,
__new__ ,
__reduce__ ,
__reduce_ex__ ,
__sizeof__ ,
__subclasshook__
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Inherited from object :
__class__
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__init__(self,
cmd=' blast_formatter ' ,
**kwargs)
(Constructor)
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Create a new instance of a command line wrapper object.
- Overrides:
object.__init__
- (inherited documentation)
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Make sure the required parameters have been set (PRIVATE).
No return value - it either works or raises a ValueError.
This is a separate method (called from __str__) so that subclasses may
override it.
- Overrides:
Application.AbstractCommandline._validate
- (inherited documentation)
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