[Biopython] NcbiblastxCommandline error

[Eric Talevich]

On Wed, Feb 9, 2011 at 5:07 PM, Gregorio Manuel Iraola Bentancor <
goyo1987 at gmail.com> wrote:

> Hello, my name is Gregorio from Uruguay. I am trying to perform some local
> blast in my machine, but I got this error:
>
> Python 2.6.5 (r265:79063, Apr 16 2010, 13:57:41)
> [GCC 4.4.3] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>> from Bio.Blast.Applications import NcbiblastxCommandline
> >>> blastx_cline = NcbiblastxCommandline(cmd='blastx',db='K10909.fasta',
> query='query.fasta',out='salida.xml')
> >>> blastx_cline()
> Traceback (most recent call last):
>  File "<stdin>", line 1, in <module>
> TypeError: 'NcbiblastxCommandline' object is not callable
>
> I do not know what is happening, because the same code runs well in other
> computers. I would really appreciate any advice or solution.
>

Hi Gregorio,

If the same code has worked on other machines, then you probably have
different versions of Biopython installed on these machines. The
"Commandline" objects became callable in Biopython version 1.55, but in
earlier versions we would first serialize the command line as a string, then
launch it as a subprocess.

Can you update the Biopython installation on your local computer? If not,
I'd recommend converting the NcbiblastxCommandline to a string --
str(blastx_cline) -- then using os.system() or subprocess.call() to execute
the command (the string).

Most of the subprocess examples have been dropped from the current tutorial,
but you can draw some inspiration for the Muscle section (look at the second
example, which uses subprocess.Popen):
http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc77


Best wishes,
Eric