<html><head><style>body{font-family:Helvetica,Arial;font-size:13px}</style></head><body><div style="font-family:Helvetica,Arial;font-size:13px">Hello biopython world,</div><div style="font-family:Helvetica,Arial;font-size:13px"><br></div><div style="font-family:Helvetica,Arial;font-size:13px">For my last job, I wrote some python code to categorize and describe sequence changes of many types. I used biopython to handle sequences and some basic functions like IO and translation, but I did not find a module for reading variants/mutants and applying them to sequences.</div><div style="font-family:Helvetica,Arial;font-size:13px"><br></div><div style="font-family:Helvetica,Arial;font-size:13px">Some cases are trivial, but some are not. For example, a small deletion in the nucleotide sequence may have no effect on the amino acid corresponding to the position of the affected codon, but will affect downstream amino acids. Protein changes caused by deletions or insertions of 3, 6, 9 . . . nucleotides can also be tricky to calculate.</div><div style="font-family:Helvetica,Arial;font-size:13px"><br></div><div style="font-family:Helvetica,Arial;font-size:13px">My question is whether there is a biopython module to read variants in a standard format (see for example <a href="http://varnomen.hgvs.org/">http://varnomen.hgvs.org/</a>)? Along with the variant objects there could be a set of methods to operate on mutated sequences. Does the community think that this would be useful if it does not already exist?</div><div style="font-family:Helvetica,Arial;font-size:13px"><br></div><div style="font-family:Helvetica,Arial;font-size:13px">I implemented many functions for these sorts of operations, but I realized soon afterwards that there are probably better ways to do much of it. I always wanted to redo the work, but never had time. Now I have time, but am not at that job. If it would be useful to the community, I may be able to take it on as a contribution to biopython.</div><div style="font-family:Helvetica,Arial;font-size:13px"><br></div><div style="font-family:Helvetica,Arial;font-size:13px">A caveat is that I don’t have experience contributing to multi-developer projects. I try to write clean, well documented code and I’m familiar with the basics of git. So, it’s OK if you’d prefer that I start with something smaller (like unit tests or documentation). Just let me know.</div><div style="font-family:Helvetica,Arial;font-size:13px"><br></div><div style="font-family:Helvetica,Arial;font-size:13px">Dave Merberg</div><br><div class="gmail_signature"></div></body></html>