<div dir="ltr">I have a code that used to work I think in 1.52 or so.<div>This is the code I am testing now in 1.76:</div><div><br></div><div><div style="color:rgb(0,0,0);background-color:rgb(255,255,254);font-family:monospace,Menlo,Monaco,"Courier New",monospace;font-size:14px;line-height:19px;white-space:pre"><div><span style="color:rgb(175,0,219)">from</span> Bio <span style="color:rgb(175,0,219)">import</span> AlignIO</div><div><span style="color:rgb(175,0,219)">from</span> Bio.Align.AlignInfo <span style="color:rgb(175,0,219)">import</span> SummaryInfo</div><div><span style="color:rgb(175,0,219)">from</span> Bio.Alphabet <span style="color:rgb(175,0,219)">import</span> ProteinAlphabet</div><br><div>align = AlignIO.read(<span style="color:rgb(163,21,21)">'samples/cas9align.fasta'</span>, <span style="color:rgb(163,21,21)">'fasta'</span>)</div><div>align._alphabet = ProteinAlphabet()</div><div>summary = SummaryInfo(align)</div><div>summary.pos_specific_score_matrix()</div></div></div><div><br></div><div>I get <br></div><div><br></div><div><pre style="margin-bottom:0px;margin-top:0px;display:inline;color:rgb(33,33,33);font-size:14px"><a href="https://localhost:8080/#">/usr/local/lib/python3.6/dist-packages/Bio/Align/AlignInfo.py</a> in _guess_consensus_alphabet(self, ambiguous)
<span style="font-weight:bold">    196</span>             if not isinstance(alt, a.__class__):
<span style="font-weight:bold">    197</span>                 raise ValueError("Alignment contains a sequence with \
--> 198                                 an incompatible alphabet.")
<span style="font-weight:bold">    199</span> 
<span style="font-weight:bold">    200</span>         # Check the ambiguous character we are going to use in the consensus

</pre><pre style="margin-bottom:0px;margin-top:0px;display:inline;color:rgb(33,33,33);font-size:14px">ValueError: Alignment contains a sequence wit an incompatible alphabet.</pre><br></div><div><br></div><div>The alignment alphabet is protein, so I don't know what is wrong with it.</div><div>This is the alignment file I am using:</div><div><a href="https://github.com/Serulab/Py4Bio/blob/master/samples/cas9align.fasta">https://github.com/Serulab/Py4Bio/blob/master/samples/cas9align.fasta</a><br></div><div><br></div><div>I will appreciate any help.</div><div><br></div><div>Best,</div><div>SB</div><div><br></div><div><br></div><div><br></div></div>