<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""><font face="Menlo" class=""><span style="font-size: 11px;" class="">Hello Everyone,</span></font></span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""><font face="Menlo" class=""><span style="font-size: 11px;" class=""><br class=""></span></font></span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""><font face="Menlo" class=""><span style="font-size: 11px;" class="">I wanted to use the ‘grant’ s</span></font></span><font face="Menlo" class=""><span style="font-size: 11px;" class="">ubstitution matrix, but when I specify this matrix in </span></font><span style="font-family: Menlo; font-size: 11px;" class="">DistanceCalculator</span><font face="Menlo" class=""><span style="font-size: 11px;" class="">, it throws a ValueError (the full error message is reproduced below). </span></font><font face="Menlo" class=""><span style="font-size: 11px;" class="">I have tested all the available </span></font><span style="font-variant-ligatures: no-common-ligatures;" class=""><font face="Menlo" class=""><span style="font-size: 11px;" class="">s</span></font></span><font face="Menlo" class=""><span style="font-size: 11px;" class="">ubstitution matrices and they all work with the exception of ‘fitch’ and ‘grant’. </span></font><span style="font-family: Menlo; font-size: 11px;" class="">These matrices are stored in the following file:</span></div><div style="margin: 0px; line-height: normal;" class=""><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""><br class=""></span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">~/anaconda/lib/python2.7/site-packages/Bio/SubsMat/</span>MatrixInfo.py</div></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures; font-size: 11px;" class=""><font face="Menlo" class=""><br class=""></font></span></div><div style="margin: 0px; line-height: normal;" class=""><font face="Menlo" class=""><span style="font-size: 11px;" class="">The fitch and grant matrices in this file look OK and I cannot see any obvious reason why these matrices are failing to load. </span></font><span style="font-family: Menlo; font-size: 11px;" class="">I would be very grateful for any suggesting for how to fix these matrices.</span></div><div style="margin: 0px; line-height: normal;" class=""><br class=""></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures; font-size: 11px;" class=""><font face="Menlo" class="">Thanks,</font></span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures; font-size: 11px;" class=""><font face="Menlo" class=""><br class=""></font></span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures; font-size: 11px;" class=""><font face="Menlo" class="">Konrad</font></span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures; font-size: 11px;" class=""><font face="Menlo" class=""><br class=""></font></span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""><font face="Menlo" class=""><span style="font-size: 11px;" class="">-------------------------------------------------------------------------------------------------------------------------------------</span></font></span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""><font face="Menlo" class=""><span style="font-size: 11px;" class="">The following was produced by Biopython </span></font></span><span style="font-family: Menlo; font-size: 11px;" class="">1.68 on Mac </span><font face="Menlo" class=""><span style="font-size: 11px;" class="">OS X installed using pip:</span></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="Menlo" class=""><span style="font-size: 11px;" class=""><br class=""></span></font></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures; font-size: 11px;" class=""><font face="Menlo" class="">>>> from Bio.Phylo.TreeConstruction import DistanceCalculator</font></span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class="">>>> calculator = DistanceCalculator('grant')</div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">Traceback (most recent call last):</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> File "<stdin>", line 1, in <module></span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> File “~/anaconda/lib/python2.7/site-packages/Bio/Phylo/TreeConstruction.py", line 411, in __init__</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> self.protein_matrices[model])</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> File “~/anaconda/lib/python2.7/site-packages/Bio/Phylo/TreeConstruction.py", line 480, in _build_protein_matrix</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> protein_matrix[aa1, aa2] = v</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> File “~/anaconda/lib/python2.7/site-packages/Bio/Phylo/TreeConstruction.py", line 222, in __setitem__</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures: no-common-ligatures" class=""> raise ValueError("Item not found.")</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">ValueError: Item not found.</span></div><div class=""><span style="font-variant-ligatures: no-common-ligatures" class=""><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""><font face="Menlo" class=""><span style="font-size: 11px;" class="">-------------------------------------------------------------------------------------------------------------------------------------</span></font></span></div><div class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""><font face="Menlo" class=""><span style="font-size: 11px;" class=""><br class=""></span></font></span></div></span></div><div class=""><span style="font-variant-ligatures: no-common-ligatures" class=""><div style="margin: 0px; line-height: normal;" class=""><br class=""></div><div class=""><font face="Menlo" class=""><span style="font-size: 11px;" class=""><br class=""></span></font></div><div class=""><font face="Menlo" class=""><span style="font-size: 11px;" class=""><br class=""></span></font></div></span></div></body></html>