<div dir="ltr">Dear Louis,<div><br></div><div>apologies for the late response, it was a long time ago I wrote the code and had to look at it to be able to answer your query.</div><div><br></div><div>I am assuming that you want to search .hhr-files from hhsearch (i.e. with multiple hits) as opposed to hhalign. If this is case, tha parser goes ca 50% of what you need, in that in captures the PDB id and also the alignment sequence, but not the midline. It would not be impossible to extend the parser to handle this, but currently, it does not. Would this be sufficient?</div><div><br></div><div>However, if you plan to process hhalign output, the parser gets everything out, including the midline.</div><div><br></div><div>Best wishes, Gabor</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Apr 22, 2020 at 2:51 PM Louis Dumas <<a href="mailto:louis.dumas@epfl.ch">louis.dumas@epfl.ch</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div lang="en-FR"><div class="gmail-m_-681714053197507197WordSection1"><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt">Dear CCTBX developers,<u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt"><u></u> <u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt">I am a postdoc at EPFL working with HHpred for homology modeling of membrane proteins.<u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt"><u></u> <u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt">I have been trying to write my own HHpred alignment parser until I found the python script under “cctbx_fork/iotbx/bioinformatics/__init__.py/” that contains an HHpred parser.<u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt"><u></u> <u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt">My goal is to correctly parse the raw HHpred output file (.hhr), which involves unwrapping every alignment, parsing out a lot of text to finally obtain something like this:<u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt"><u></u> <u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt">>pdb_name<u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt">query-sequence<u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt">column score<u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt"><u></u> <u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt">Example:<u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt"><u></u> <u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt">>4U15<u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt">VYGFIGGIFGFMSIMTMAMISIDRYNVIGRPMAASKKMSHRRAFIMIIFVWLWS<u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt">+........+..+..++|+++|++++.++.+.++++ +..+.++.+|+++|++.++...+........ +...|..<u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt"><u></u> <u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt"><u></u> <u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt">Being somewhat new to python, I was wondering whether the people who wrote this script are still around and could help me figure out whether the parser could be implemented in such a way.<u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt"><u></u> <u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt">Thanks for any help you can provide!<u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt"><u></u> <u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt">Best,<u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt"><u></u> <u></u></span></p><p class="MsoNormal"><span lang="EN-US" style="font-size:11pt">Louis D<u></u><u></u></span></p></div></div>
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