<div dir="ltr"><div class="gmail_default" style="font-family:comic sans ms,sans-serif">Hello,</div><div class="gmail_default" style="font-family:comic sans ms,sans-serif"><br></div><div class="gmail_default" style="font-family:comic sans ms,sans-serif">Biopython & SearchIO user for over three weeks.</div><div class="gmail_default" style="font-family:comic sans ms,sans-serif"><br></div><div class="gmail_default" style="font-family:comic sans ms,sans-serif">OS - Ubuntu 14,04</div><div class="gmail_default" style="font-family:comic sans ms,sans-serif">Biopython Bio.__version__ 1.65</div><div class="gmail_default" style="font-family:comic sans ms,sans-serif">HMMER -- 3.1b2<br></div><div class="gmail_default" style="font-family:comic sans ms,sans-serif">Code is <b><a href="https://github.com/gprakhar/scripts-biopython/tree/alpha" target="_blank">here</a></b> (github) - branch alpha</div><div class="gmail_default" style="font-family:comic sans ms,sans-serif"><br></div><div class="gmail_default" style="font-family:comic sans ms,sans-serif">Briefly, if a hmmer 3 text output is parsed using the 'SearchIO.parse()' and that file has output from more than one searches only the first result is read and rest are ignored.</div><div class="gmail_default" style="font-family:comic sans ms,sans-serif"><br></div><div class="gmail_default" style="font-family:comic sans ms,sans-serif">Details -- Used 'hmmsearch' with pfam models against a database of proteins. Since I wanted to club some domain models together, hence concatenated the result into a single text file. As all the domains concatenated together belong to a single protein.</div><div class="gmail_default" style="font-family:comic sans ms,sans-serif"><br></div><div class="gmail_default" style="font-family:comic sans ms,sans-serif">When I use SearchIO.parse() to read this file, the Queryresult object has only the top entry (first hmm models result), iterating over the Queryresult does not give the other results.</div><div class="gmail_default" style="font-family:comic sans ms,sans-serif"><br></div><div class="gmail_default" style="font-family:comic sans ms,sans-serif">To test this I have split the results file to have the results of a single hmmsearch run in each file, after this parse works fine.</div><div class="gmail_default" style="font-family:comic sans ms,sans-serif">But this use case (single result in one file) is for 'SearchIO.read()'. Consequently I would expect 'SearchIO.parse()' to be able to parse multiple results from a single file.</div><div><br></div><div><div class="gmail_default"><font face="comic sans ms, sans-serif">As test case from my <a href="https://github.com/gprakhar/scripts-biopython/tree/alpha" target="_blank">repo</a>, first run the script '</font><span style="font-family:arial,sans-serif">hmmer-SearchIO-text-parser.py', the output file '</span>Q9UP38.out' would be read </div><div class="gmail_default"> this represents the use case in which the result file has multiple (2) entries.</div></div><div class="gmail_default"><br></div><div class="gmail_default">Are my expectations from 'SearchIO.parse()' correct ? Or am I missing something ?</div><div><br></div><div><div class="gmail_default" style="font-family:'comic sans ms',sans-serif">Reply, Comments, Pointers etc. are all welcome.</div><div class="gmail_default" style="font-family:'comic sans ms',sans-serif"><span style="font-family:arial,sans-serif"><br></span></div><div class="gmail_default" style="font-family:'comic sans ms',sans-serif"><span style="font-family:arial,sans-serif">-- </span></div></div><div>Thanking you,<br>-- <br>Prakhar Gaur<br><br></div>
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