Question: Emboss Needle From Biopython, No Output File
1
gravatar for Maria
4.6 years ago by
Maria150
Maria150 wrote:

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.

windows biopython • 2.6k views
ADD COMMENTlink modified 15 months ago by Biostar ♦♦ 20 • written 4.6 years ago by Maria150
1

you need to add to first script

stdout,stderr=needle_cline()
ADD REPLYlink written 2.8 years ago by Medhat7.6k
0
gravatar for Maria
4.6 years ago by
Maria150
Maria150 wrote:

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

ADD COMMENTlink written 4.6 years ago by Maria150
1

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

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by David W4.7k
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