linearturbofold

#!/usr/bin/env python3

from genericpath import exists
import gflags as flags
#import subprocess
import sys
import os

FLAGS = flags.FLAGS

def setgflags():
    flags.DEFINE_string("input", "", "input file must in the fasta format", short_name='i')
    flags.DEFINE_string("outDir", "", "output directory for predicted MSA and structures", short_name='o')
    flags.DEFINE_integer("iter", 3, "set the number of iteration, (DEFAULT=3)", short_name='it')
    flags.DEFINE_integer("hmmBeam", 100, "set beam size for LinearAlignment, (DEFAULT=-1, infinite beam size)", short_name='b1')
    flags.DEFINE_integer("ckyBeam", 100, "set beam size for LinearPartition, (DEFAULT=100)", short_name='b2')
    flags.DEFINE_boolean("saveBFs", False, "save Partition Function after the last iteraction, (DEFAULT=False)", short_name='pf')
    flags.DEFINE_boolean("saveBPPs", False, "save base pair probabilities after the last iteraction, (DEFAULT=False)", short_name='bpp')
    flags.DEFINE_boolean("verbose", False, "print more alignment, folding and runtime information, (DEFAULT=FALSE)", short_name='v')
    flags.DEFINE_integer("TnMinHelixLength", 3, "set the min. length of helix in predicted structures in ThreshKnot, (DEFAULT=3)", short_name='tkhl')
    flags.DEFINE_integer("TnIterations", 1, "set the number of iteration of ThreshKnot, (DEFAULT=1)", short_name='tkit')
    flags.DEFINE_float("Threshold", 0.3, "set Threshold for ThreshKnot, (DEFAULT=0.3)", short_name='th')
   
    argv = FLAGS(sys.argv)

def main():
    input_file = FLAGS.input
    output_dir = FLAGS.outDir
    iteration = FLAGS.iter
    hmm_beam = str(FLAGS.hmmBeam)
    cky_beam = str(FLAGS.ckyBeam)
    is_save_pfs = "1" if FLAGS.saveBFs else "0"
    is_save_bpps = "1" if FLAGS.saveBPPs else "0"
    is_verbose = "1" if FLAGS.verbose else "0"
    TkMinHelixLength = str(FLAGS.TnMinHelixLength)
    TkIterations = str(FLAGS.TnIterations)
    Threshold = str(FLAGS.Threshold)

    if not input_file: 
        print("Do not provide the input file (should in the fasta format).")
        exit()
    
    if not os.path.exists(output_dir):
       os.mkdir(output_dir)
 
    if iteration < 0:
        print("Invalid TurboFold iterations given.")

    path = os.path.dirname(os.path.abspath(__file__))
    input_file = os.path.abspath(input_file)
    output_dir = os.path.abspath(output_dir)
    cmd = ["cd %s; %s/%s" % (path, path, 'bin/linearturbofold'), input_file, output_dir, hmm_beam, cky_beam, str(iteration), is_save_bpps, is_save_pfs, is_verbose, TkMinHelixLength, TkIterations, Threshold]
    cmd=' '.join(cmd)
    os.system(cmd)
    #subprocess.call(cmd)
    
if __name__ == '__main__':
    setgflags()
    main()