Class NcbiblastnCommandline
source code
object --+
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Application.AbstractCommandline --+
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_NcbiblastCommandline --+
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_Ncbiblast2SeqCommandline --+
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NcbiblastnCommandline
Wrapper for the NCBI BLAST+ program blastn (for nucleotides).
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 blastn.
For example, to run a search against the "nt" nucleotide
database using the FASTA nucleotide file "m_code.fasta" as the
query, with an expectation value cut off of 0.001, saving the output to a
file in XML format:
>>> from Bio.Blast.Applications import NcbiblastnCommandline
>>> cline = NcbiblastnCommandline(query="m_cold.fasta", db="nt", strand="plus",
... evalue=0.001, out="m_cold.xml", outfmt=5)
>>> cline
NcbiblastnCommandline(cmd='blastn', query='m_cold.fasta', db='nt', out='m_cold.xml', evalue=0.001, outfmt=5, strand='plus')
>>> print cline
blastn -query m_cold.fasta -db nt -out m_cold.xml -evalue 0.001 -outfmt 5 -strand plus
You would typically run the command line with the Python subprocess
module, as described in the Biopython tutorial.
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__init__(self,
cmd=' blastn ' ,
**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=' blastn ' ,
**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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