Class NcbiblastxCommandline
source code
object --+
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Application.AbstractCommandline --+
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_NcbibaseblastCommandline --+
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_NcbiblastCommandline --+
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_Ncbiblast2SeqCommandline --+
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_NcbiblastMain2SeqCommandline --+
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NcbiblastxCommandline
Wrapper for the NCBI BLAST+ program blastx (nucleotide query, protein
database).
With the release of BLAST+ (BLAST rewritten in C++ instead of C), the
NCBI replaced the old blastall tool with separate tools for each of the
searches. This wrapper therefore replaces BlastallCommandline with option
-p blastx.
>>> from Bio.Blast.Applications import NcbiblastxCommandline
>>> cline = NcbiblastxCommandline(query="m_cold.fasta", db="nr", evalue=0.001)
>>> cline
NcbiblastxCommandline(cmd='blastx', query='m_cold.fasta', db='nr', evalue=0.001)
>>> print cline
blastx -query m_cold.fasta -db nr -evalue 0.001
You would typically run the command line with cline() or via the
Python subprocess module, as described in the Biopython tutorial.
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__init__(self,
cmd=' blastx ' ,
**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=' blastx ' ,
**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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