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<div class="">Hi All,</div>
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<div class="">I am using the MUSCLE command line wrapper for pairwise sequence alignments (using StringIO but that isn’t the issue here…).</div>
<div class="">It works nicely, until I try to specify a gapextend penalty. It seems that this Option was neglected in the command line wrapper?</div>
<div class="">The Option does exist in the MUSCLE docs: <a href="http://www.drive5.com/muscle/muscle_userguide3.8.html" class="">http://www.drive5.com/muscle/muscle_userguide3.8.html</a></div>
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<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>records = [SeqRecord(full_ref_seq,id="ref"),SeqRecord(full_fit_seq,id="fit")]</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>muscle_cline = MuscleCommandline(clwstrict=True, matrix='blosum62', gapopen=-11.0, gapextend=-1.0, center=0.0)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>child = subprocess.Popen(str(muscle_cline),</div>
<div class=""> stdin=subprocess.PIPE,</div>
<div class=""> stdout=subprocess.PIPE,</div>
<div class=""> stderr=subprocess.PIPE,</div>
<div class=""> universal_newlines=True,</div>
<div class=""> shell=(sys.platform!="win32"))</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>SeqIO.write(records, child.stdin, "fasta")</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>child.stdin.close()</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>align = AlignIO.read(child.stdout, format="clustal”)</div>
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<pre style="box-sizing: border-box; overflow: auto; font-size: 14px; padding: 0px; margin-top: 0px; margin-bottom: 0px; line-height: inherit; word-break: break-all; word-wrap: break-word; background-color: rgb(255, 255, 255); border: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; border-bottom-right-radius: 0px; border-bottom-left-radius: 0px; white-space: pre-wrap; vertical-align: baseline; orphans: 2; widows: 2;" class=""><span class="ansicyan" style="box-sizing: border-box; color: steelblue;"><span class="ansigreen" style="box-sizing: border-box; color: darkgreen;"><span class="ansicyan" style="box-sizing: border-box; color: steelblue;"><span class="ansigreen" style="box-sizing: border-box; color: darkgreen;"><span class="ansicyan" style="box-sizing: border-box; color: steelblue;"><span class="ansicyan" style="box-sizing: border-box;"><span class="ansigreen" style="box-sizing: border-box; color: darkgreen;"><span class="ansicyan" style="box-sizing: border-box; color: steelblue;"><span class="ansigreen" style="box-sizing: border-box; color: darkgreen;"><span class="ansicyan" style="box-sizing: border-box; color: steelblue;"><span class="ansigreen" style="box-sizing: border-box; color: darkgreen;"><span class="ansicyan" style="box-sizing: border-box; color: steelblue;"><span class="ansicyan" style="box-sizing: border-box;"><span class="ansigreen" style="box-sizing: border-box; color: darkgreen;"><span class="ansicyan" style="box-sizing: border-box; color: steelblue;"><span class="ansigreen" style="box-sizing: border-box; color: darkgreen;"><span class="ansicyan" style="box-sizing: border-box; color: steelblue;"><span class="ansigreen" style="box-sizing: border-box; color: darkgreen;"><span class="ansired" style="box-sizing: border-box; color: darkred;"><span class="ansired" style="box-sizing: border-box;">ValueError</span>: Option name gapextend was not found.</span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></pre>
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<div class="">Upon inspecting the muscle_cline object, this kwarg is indeed absent (it exists in the analogous clustal wrapper).</div>
<div class="">print dir(muscle_cline)</div>
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<pre style="box-sizing: border-box; overflow: auto; font-size: 14px; padding: 0px; margin-top: 0px; margin-bottom: 0px; line-height: inherit; word-break: break-all; word-wrap: break-word; background-color: rgb(255, 255, 255); border: 0px; border-top-left-radius: 0px; border-top-right-radius: 0px; border-bottom-right-radius: 0px; border-bottom-left-radius: 0px; white-space: pre-wrap; vertical-align: baseline; orphans: 2; widows: 2;" class="">['__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', <b class="">'gapopen'</b>, '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']</pre>
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<div class="">Is there another way around this? Any help would be much appreciated.</div>
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<div class="">Thanks in advance,</div>
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<div class="">Josh</div>
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