Emboss Needle From Biopython, No Output File

Question

[Maria]

I am trying to use emboss from biopython, I copied into the python commandline the commands from the link above i.e :

>>> from Bio.Emboss.Applications import NeedleCommandline
>>> needle_cline = NeedleCommandline(asequence="alpha.faa", bsequence="beta.faa", gapopen=10, gapextend=0.5, outfile="needle.txt")

I don't get any error message but the problem is that the file needle.txt is not created and when executing the code below I get an error as the needle.txt file can't be found:

>>> from Bio import AlignIO
>>> align = AlignIO.read("needle.txt", "emboss")
>>> print(align)

Please any idea what is wrong here ? Note that the graphical interface Jemboss works well and I can align and see the output.

[Medhat]

you need to add to first script

stdout,stderr=needle_cline()

Answer 1

[Maria]

The Code above give a command that have to be executed manually

[David W]

Not only manually, you can also call the Commandline object you made with needle_cline()