Question: Biopython Emboss Needle gives no output file
0
gravatar for weihan
2.2 years ago by
weihan0
weihan0 wrote:

I'm learning Emboss Needle from biopython to align two sequences. When I type in the following comments(used as an example from Biopython cookbook):

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

It returns: needle -outfile=needle.txt -asequence=alpha.faa -bsequence=beta.faa -gapopen=10 -gapextend=0.5

However, no output file named "needle.txt" is generated. All input files are present. No errors msg appear in the process. Anyone knows what went wrong? Thanks!

alignment • 932 views
ADD COMMENTlink modified 2.2 years ago by Asaf5.5k • written 2.2 years ago by weihan0
2
gravatar for a.zielezinski
2.2 years ago by
a.zielezinski8.6k
a.zielezinski8.6k wrote:

You just created a needle command line object without actually running the program :)

To run the command, type:

stdout, stderr = needle_cline()
print(stdout + stderr)

The output file needle.txt should be right there for you. For more information, read the whole 6.4.5. section (EMBOSS needle and water) in the BioPython Tutorial and Cookbook.

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by a.zielezinski8.6k

Thank you! However, when I type in

stdout, stderr = needle_cline()

It returns:

Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Bio/Application/__init__.py", line 516, in __call__ stdout_str, stderr_str) Bio.Application.ApplicationError: Non-zero return code 127 from 'needle -outfile=needle.txt -asequence=alpha.faa -bsequence=beta.faa -gapopen=10 -gapextend=0.5', message '/bin/sh: needle: command not found'

Is there something wrong with PATH?

ADD REPLYlink written 2.2 years ago by weihan0

Probably. It can't find needle in default $PATH.

ADD REPLYlink written 2.2 years ago by Asaf5.5k
1
gravatar for Asaf
2.2 years ago by
Asaf5.5k
Israel
Asaf5.5k wrote:

Keep reading the cookbook, you should execute this line.

ADD COMMENTlink written 2.2 years ago by Asaf5.5k
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