<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hello everyone,<div><br><div>I am trying to model secondary structures of some RNA.</div><div><br></div><div>As I am not an expert in programming it is quite a challenge for me so far I found a way to access RNAfold from biopython via biomanycores.</div><div><br></div><div>I downloaded and installed both biomanycores and RNAfold tools in </div><div>/usr/local/bin/</div><div><br></div><div>and wrote a simple test script in python before loading my dataset</div><div><br></div><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;"><blockquote type="cite"><div>from Biomanycores import RNAFold</div><div><br></div><div>RNA = 'CUGCAUUGGCCAAAUUGGCCCUACUACGUAUGCUAGCAUGAGAUGUGACAGUACAGUGUACUUAC'</div><div><br></div><div>structure = RNAFold.execute(RNA)</div><div><br></div><div>print(structure)</div></blockquote></blockquote><div><br></div><div> </div><div>Unfortunately it hasn’t work and generated this error message:</div><div><br></div><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><blockquote type="cite">Traceback (most recent call last):</blockquote></div><div><blockquote type="cite"> File "/Users/user/Google Drive/Bioinformatics/smallRNAseq/Python secondary structure/RNAFoldtest", line 9, in <module></blockquote></div><div><blockquote type="cite"> structure = RNAFold.execute(RNA)</blockquote></div><div><blockquote type="cite"> File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Biomanycores-1.1210-py2.7.egg/Biomanycores/RNAFold.py", line 221, in execute</blockquote></div><div><blockquote type="cite"> handle, delta = rnafold_cmd.run(verbose=verbose)</blockquote></div><div><blockquote type="cite"> File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Biomanycores-1.1210-py2.7.egg/Biomanycores/AbstractCommandline.py", line 141, in run</blockquote></div><div><blockquote type="cite"> stderr=stderr_str)</blockquote></div><div><blockquote type="cite">ApplicationError: Non-zero return code 1 from '/usr/local/bin/RNAfold -f', message '/usr/local/bin/RNAfold: invalid option -- f'</blockquote></div></blockquote><br><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><blockquote type="cite">>>> </blockquote></div></blockquote><div><br></div>Do you know any solution for my problem? Alternatively maybe you know of some different approach to analyse secondary structure with biopython?<div><br></div><div>All best,</div><div><br></div><div>Jakub</div></div></body></html>