I am trying to use emboss from biopython, I copied into the python commandline the commands from the link above i.e :
>>> from Bio.Emboss.Applications import NeedleCommandline >>> needle_cline = NeedleCommandline(asequence="alpha.faa", bsequence="beta.faa", gapopen=10, gapextend=0.5, outfile="needle.txt")
I don't get any error message but the problem is that the file needle.txt is not created and when executing the code below I get an error as the needle.txt file can't be found:
>>> from Bio import AlignIO >>> align = AlignIO.read("needle.txt", "emboss") >>> print(align)
Please any idea what is wrong here ? Note that the graphical interface Jemboss works well and I can align and see the output.