[Biopython] MUSCLE gap extend penalty

[Joshua Meyers]

Hi All,

I am using the MUSCLE command line wrapper for pairwise sequence alignments (using StringIO but that isn’t the issue here…).
It works nicely, until I try to specify a gapextend penalty. It seems that this Option was neglected in the command line wrapper?
The Option does exist in the MUSCLE docs: http://www.drive5.com/muscle/muscle_userguide3.8.html

records = [SeqRecord(full_ref_seq,id="ref"),SeqRecord(full_fit_seq,id="fit")]
muscle_cline = MuscleCommandline(clwstrict=True, matrix='blosum62', gapopen=-11.0, gapextend=-1.0, center=0.0)
child = subprocess.Popen(str(muscle_cline),
                         stdin=subprocess.PIPE,
                         stdout=subprocess.PIPE,
                         stderr=subprocess.PIPE,
                         universal_newlines=True,
                         shell=(sys.platform!="win32"))
SeqIO.write(records, child.stdin, "fasta")
child.stdin.close()
align = AlignIO.read(child.stdout, format="clustal”)


ValueError: Option name gapextend was not found.

Upon inspecting the muscle_cline object, this kwarg is indeed absent (it exists in the analogous clustal wrapper).
print dir(muscle_cline)

['__call__', '__class__', '__delattr__', '__dict__', '__doc__', '__format__', '__getattribute__', '__hash__', '__init__', '__module__', '__new__', '__reduce__', '__reduce_ex__', '__repr__', '__setattr__', '__sizeof__', '__str__', '__subclasshook__', '__weakref__', '_check_value', '_clear_parameter', '_get_parameter', '_validate', 'anchors', 'anchorspacing', 'center', 'cluster1', 'cluster2', 'clw', 'clwout', 'clwstrict', 'clwstrictout', 'core', 'diaglength', 'diagmargin', 'diags', 'distance1', 'distance2', 'fasta', 'fastaout', 'gapopen', 'group', 'html', 'htmlout', 'hydro', 'hydrofactor', 'in1', 'in2', 'input', 'le', 'log', 'loga', 'maxdiagbreak', 'maxhours', 'maxiters', 'maxtrees', 'minbestcolscore', 'minsmoothscore', 'msf', 'msfout', 'noanchors', 'nocore', 'objscore', 'out', 'parameters', 'phyi', 'phyiout', 'phys', 'physout', 'profile', 'program_name', 'quiet', 'refine', 'root1', 'root2', 'seqtype', 'set_parameter', 'smoothscoreceil', 'smoothwindow', 'sp', 'spn', 'stable', 'sueff', 'sv', 'tree1', 'tree2', 'verbose', 'version', 'weight1', 'weight2']


Is there another way around this? Any help would be much appreciated.

Thanks in advance,

Josh

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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