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!