I'm new to biopython and trying to run the example provided by the biopython documentation section 6.4.5 EMBOSS needle and water:
from Bio.Emboss.Applications import NeedleCommandline needle_cline = NeedleCommandline(asequence="alpha.fasta", bsequence="beta.fasta", gapopen=10, apextend=0.5,outfile="needle.txt") stdout,stderr=needle_cline()
I have created two .fasta files and saved two sequences in FASTA format and named the files alpha.fasta and beta.fasta respectively in the same directory as the script containing the above given example. whenever it executes the last line ("stdout,stderr=needle_cline()") it's giving the following error:
Traceback (most recent call last): File "<stdin>", line 1, in <module> File "C:\Anaconda\lib\site-packages\Bio\Application\__init__.py", line 513, in __call__ stdout_str, stderr_str) Bio.Application.ApplicationError: Non-zero return code 1 from 'needle -outfile=needle.txt -asequence=alpha.fasta -bsequence=beta.fasta -gapopen=10 -gapextend=0.5', message "'needle' is not recognized as an internal or external command,"
I can't figure out why I'm not able to run this simple example, also it is not creating the output file named "needle.txt"
Thanks in advance