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lorenzo-rovigatti / tacoxDNA

A collection of tools for DNA modelling
http://tacoxdna.sissa.it/
GNU General Public License v3.0
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Cannot set sequence in cadnano_oxDNA.py #12

Open FerdinandoR opened 4 years ago

FerdinandoR commented 4 years ago

I'm trying to use the script cadnano_oxDNA.py to take a design and sequence file generated with cadnano, instead of randomly generating one. However, I'm unable to do so - it seems that the option only takes out the sequences of the vhelix, rather than the sequence of the staple, which is not an output from cadnano.

Is there a way to meaningfully transfer the sequence from CadNano to OxDNA through tacoxDNA?

MishraS-S commented 4 years ago

I am also interested in this thread. This probably isn't an issue to be honest since I'm assuming the --sequence option works as intended. The problem the both of us seem to be facing is that the only way to export any form of sequence information from within cadnano2 seems to the be export sequence option which outputs a csv with the sequences of all the staple strands. This is not accepted as a valid sequence file by cadnano_oxDNA.py. Indeed the documentation (which I found for cadnano_interface.py but this looks like it is the predecessor/precursor to the one in tacoxDNA) states that, " That file should contain a letter (A,T,G,C or R for random) designating the sequence of the scaffold strand, for every pair of squares (which denote a base pair) in the cadnano design. This includes squares that do not contain a strand. So the sequence file should be an M by N grid of letters where M is the length of the helices and N is the number of helices in the cadnano design (including entirely unoccupied rows). Note that there is no need to include skips in the sequence file. " I think what we would like to know if there is a way generate this kind of a file possibly from within cadnano or via an external tool. I tried searching for this information in the docs for tacoxDNA and the scripts that come with oxDNA for eg. origami_utils, but wasn't able to glean anything. I apologise if this has been addressed elsewhere already.

MishraS-S commented 4 years ago

Just to update anyone looking at this in the future, wrote a quick script to do this https://github.com/Mishrito/oxDNA-handy-scripts/blob/master/json_to_sqs_tacoxdna.py