<div dir="ltr"><span style="font-family:arial,sans-serif;font-size:13px">Hi all,</span><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">I have written an interface to the BOLD database of DNA barcodes. It accepts FASTA files, sends them to BOLD and gets the specimen identifications to the species level:<br><br><a href="https://github.com/carlosp420/bold_retriever" target="_blank">https://github.com/carlosp420/bold_retriever</a></div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">I was wondering whether it could be included into BioPython? So far the packages is a bunch of scripts and I want to make it more robust.</div><div style="font-family:arial,sans-serif;font-size:13px">The working version is not so efficient as the running time has exponential growth (n squared).</div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">However, I was able to use asynchronous calls (using Twisted) to make it faster. The script was able to take (n) seconds for (n) number of sequences. But I don't fully understand Twisted and the package is unstable.</div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">So, I wanted to ask if this little project of mine has any hope of getting into BioPython. If that is the case I would need some pointers on using proper classes for the code and fixing the code so that it can be integrated. I guess I would need to drop Twisted and use instead a standard Python library for multithreading.</div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">I want to improve the package anyways, make it more robust and quick. So I wanted to ask before giving another chance to Twisted.</div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">Any comments would be appreciated,</div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">carlos</div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div><div>Dr. Carlos Peña<br>Laboratory of Genetics<br>Department of Biology<br>University of Turku<br>20014 Turku<br>FINLAND<br><div><br></div></div></div>
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