gravatar for Thesnak

2 hours ago by

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:mEMBOSSneedle.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:Usersmohamanaconda3libsite-packagesBioApplication__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'



Source link