mrparse.mr_deepcoil module

Created on 18 Oct 2018

@author: jmht

class CCPred(seq_info, deepcoil_exe)

Bases: object

Class to run Coiled-coil prediction using Deepcoil: https://github.com/labstructbioinf/DeepCoil

As Deepcoil has a length limit of 30 < 500 residues, anything over 500 we need to split into chunks

Notes: The sequence code should be numpified

get_prediction()

parse_deepcoil(outfile)

probabilites_from_sequence(seq_info, deepcoil_exe)

run_deepcoil(seq_info, deepcoil_exe)

run deepcoil and return the ouptut file

Currently the deepcoil script has no argument to specify the filename and automatically takes it from the header of the fasta. As it will mangle the name to ensure a valid filename is produced, it makes it hard to know what the file will be called. We therefore write out our own fasta file with a set header so we know what the file will be called.