Class NcbiblastpCommandline
source code
object --+
|
Application.AbstractCommandline --+
|
_NcbiblastCommandline --+
|
_Ncbiblast2SeqCommandline --+
|
NcbiblastpCommandline
Create a commandline for the NCBI BLAST+ program blastp (for
proteins).
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 blastp.
>>> from Bio.Blast.Applications import NcbiblastpCommandline
>>> cline = NcbiblastpCommandline(query="rosemary.pro", db="nr",
... evalue=0.001, remote=True, ungapped=True)
>>> cline
NcbiblastpCommandline(cmd='blastp', query='rosemary.pro', db='nr', evalue=0.001, remote=True, ungapped=True)
>>> print cline
blastp -query rosemary.pro -db nr -evalue 0.001 -remote -ungapped
You would typically run the command line with the Python subprocess
module, as described in the Biopython tutorial.
|
__init__(self,
cmd=' blastp ' ,
**kwargs)
Create a new instance of a command line wrapper object. |
source code
|
|
|
|
Inherited from Application.AbstractCommandline :
__repr__ ,
__setattr__ ,
__str__ ,
set_parameter
Inherited from object :
__delattr__ ,
__format__ ,
__getattribute__ ,
__hash__ ,
__new__ ,
__reduce__ ,
__reduce_ex__ ,
__sizeof__ ,
__subclasshook__
|
Inherited from object :
__class__
|
__init__(self,
cmd=' blastp ' ,
**kwargs)
(Constructor)
| source code
|
Create a new instance of a command line wrapper object.
- Overrides:
object.__init__
- (inherited documentation)
|
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)
|