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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D">Hi all,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D">Two questions –<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-.25in"><span style="font-size:10.0pt;font-family:Symbol;color:#1F497D">·</span><span style="font-size:7.0pt;font-family:"Times New Roman","serif";color:#1F497D">
</span><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D">Can CAPSMap() take an alignment that has gaps? I see errors both if the alignment has gap characters and if there are no gaps but the sequences are of different lengths.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-.25in"><span style="font-size:10.0pt;font-family:Symbol;color:#1F497D">·</span><span style="font-size:7.0pt;font-family:"Times New Roman","serif";color:#1F497D">
</span><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D">What role does upper/lower case play in alignments? BioPython test alignment sequences are gapless and mixed case. Wondering what I’m missing here, especially regarding gaps. A
pointer to documentation would be great.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D">Background –<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D">I am having some difficulty understanding/using the Bio.CAPS module. If I pass in an alignment with gap characters into CAPSMAP() and call ._digest_with() on it, I receive
an invalid character error. When I remove the offending characters (‘-‘ and ‘.’), I receive an error from the AlignIO.read() method that the lengths of the sequences are not the same. I looked at the provided test file (test_CAPS.py), and noticed that the
aligned sequences do not contain gap characters and that the sequences also contain lowercase letters. Is this module only workable if the alignment has no gap characters and has the same length? And what role does case play in these aligned sequences?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D">Here is the script I ran:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D">from Bio.CAPS import DifferentialCutsite
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D">from Bio.CAPS import CAPSMap<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D">from Bio import AlignIO<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D">from Bio.Restriction import *<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D">def main():<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D"> alignment = AlignIO.read("gap_chars.txt", "fasta")<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D"> map = CAPSMap(alignment)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D"> enzymes = [EcoRI]<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D"> for enzyme in enzymes:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D"> map._digest_with(enzyme)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D">main()<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D">Here are the 2 data files I ran:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D">Data file 1: “gap_chars.txt”<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D">>gi|2695850|emb|Y13260.1|ABY13260/1-573<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D">TCTGCTGGTTACAACACTTTCTTCTTTCAATAAC.CACAATACTGCAGTACAATGG.GGA<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D">>gi|2695854|emb|Y13264.1|ABY13264/1-547<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D">.................TTTCTTCTTTCAATAAC.CACAATACTGCAGTACAATGG.GGA<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D">Data file 2: “no_gaps.txt”<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D">>gi|2695850|emb|Y13260.1|ABY13260 Acipenser baeri mRNA for immunoglobulin heavy chain, clone ScH 16.1<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D">TCTGCTGGTTACAACACTTTCTTCTTTCAATAACCACAATACTGCAGTACAATGGGGA<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D">>gi|2695854|emb|Y13264.1|ABY13264 Acipenser baeri mRNA for immunoglobulin heavy chain, clone ScH 113<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D">TTTCTTCTTTCAATAACCACAATACTGCAGTACAATGGGGA<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D">If someone could better help me understand how to use this module I’d greatly appreciate it!
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D">Regards,
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New";color:#1F497D">Esther<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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