EMBOSS dosen't output file in biopython
I tried to execute this code using biopython but there is no file for output
from Bio.Emboss.Applications import NeedleCommandline
needle_cline=NeedleCommandline(r"C:\mEMBOSS\needle.exe",asequence="Sequence 1.txt",bsequence="Sequence 2.txt",gapopen=10,gapextend=0.5,outfile="output.txt")
stdout,stderr = needle_cline()
error:
Traceback (most recent call last):
File "F:/Study/Bioinformatics/Level 3/Term 1/Bio Computing/Assignment/Assignment 2/Main.py", line 4, in <module>
stdout,stderr = needle_cline()
File "C:\Users\moham\anaconda3\lib\site-packages\Bio\Application\__init__.py", line 569, in __call__
raise ApplicationError(return_code, str(self), stdout_str, stderr_str)
Bio.Application.ApplicationError: Non-zero return code 1 from 'C:\\mEMBOSS\\needle.exe -outfile=output.txt -asequence="Sequence 1.txt" -bsequence="Sequence 2.txt" -gapopen=10 -gapextend=0.5', message 'Died: EMBOSS_ROOT must be defined for Windows'
• 1,293 views
•
link
updated
by
Mensur Dlakic
•
written
by
Thesnak •
•
written
by
Thesnak •
1 answer
The error message tells you what is wrong: 'Died: EMBOSS_ROOT must be defined for Windows'. That means you need to tell the system where EMBOSS files are, which for you seems to be C:\mEMBOSS\. Google windows path variable to find out how to add EMBOSS_ROOT to it.
• 0 views
•
link
written
by
Mensur Dlakic
Log in to answer this question.
More posts like this
-
Multiple Sequence Alignment using MUSCLE tool in biopython
written by unicorn2kang •
-
Non-zero return code 127 from Needle
written by Park •
-
Biopython Emboss Needle gives no output file
written by weihan •
-
can not get the alignment result from needle alignment
written by Medhat
-
alignment using needleman wunsch in biopython
written by sumithrasank75
-
EMBOSS needle question
written by mossig89 •
-
EMBOSS needle question
written by mossig89 •
-
Emboss In Biopython Asequence And Bsequence
written by Maria •
-
The Biopython Needlecommandline Class Complains About Needle Returning Non-Zero
written by jergosh
-
Global Pairwise Alignment For Long Sequence Throws Error In Python!!
written by abhishekniroula7
Do yourself a favour and get used to NOT using whitespaces in folder names, paths and file names. Use underscores or camelcases.