python - Biopython/EMBOSS WindowsError [Error 2] -


i trying locally align set of around 100, long (>8000 sequence) sequences using biopython wrapper emboss.

essentially need locally align each sequence in fasta file against every other sequence in fasta file. far have tried run basic code below:

from bio.emboss.applications import needlecommandline bio import alignio  seq_fname1 = 'gross-alignment.fasta' seq_fname2 = 'gross-alignment.fasta' needle_fname = 'pairwise_output.txt' needle_cli = needlecommandline(asequence=seq_fname1, \                                bsequence=seq_fname2, \                                gapopen=10, \                                gapextend=0.5, \                                outfile=needle_fname)  """this generates needle file""" needle_cli()  """that parses needle file, aln[0] , aln[1] contain aligned first , second sequence in usual format (e.g. - gap)""" aln = alignio.read(needle_file, "emboss")  print aln

but following error when so:

c:\windows\system32\cmd.exe /c (python ^<c:\users\user\appdata\local\temp\viiaad1.tmp) traceback (most recent call last): file "<stdin>", line 14, in <module> file "c:\python27\lib\site-packages\bio\application\__init__.py", line 495, in __call__ shell=use_shell) file "c:\python27\lib\subprocess.py", line 711, in __init__ errread, errwrite) file "c:\python27\lib\subprocess.py", line 959, in _execute_child startupinfo) windowserror: [error 2] system cannot find file specified shell returned 1 hit key close window...

i can't figure cause of error is, appreciated.

can try absolute paths seq_fname1, seq_fname2 well? also, hope trying out in elevated command prompt

moving answer comments :)


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