comparison PDAUG_AA_Property_Based_Peptide_Generation/PDAUG_AA_Property_Based_Peptide_Generation.py @ 6:92bdc5cbf028 draft

"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"

5:20a0454c5347

        OutPep = amphi_hel.sequences
        
        for i,O in enumerate(OutPep):
            OutFasta.write(">sequence_"+str(i)+'\n')
            OutFasta.write(O+'\n')

if __name__=='__main__':

    parser = argparse.ArgumentParser(description='Deployment tool')
    subparsers = parser.add_subparsers()

    Arc.add_argument("-m","--lenmin_s", required=False, default=7, help="")
    Arc.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max")
    Arc.add_argument("-a","--arcsize", help="Choose among 100, 140, 180, 220, 260, or choose mixed to generate a mixture")
    Arc.add_argument("-y","--hyd_gra", default='False', help="Method to mutate the generated sequences to have a hydrophobic gradient by substituting the last third of the sequence amino acids to hydrophobic.")
    Arc.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta")

    args = parser.parse_args()

    if sys.argv[1] == 'Random':
        Random_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.S_proba, args.OutFasta)

        Hepahelices_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.OutFasta)
    elif sys.argv[1] == 'AMPngrams':
        AMPngrams_seq(args.seq_num, args.n_min, args.n_max, args.OutFasta)
    elif sys.argv[1] == 'AmphipathicArc':
        AmphipathicArc_seq(int(args.seq_num), int(args.lenmin_s), int(args.lenmax_s), int(args.arcsize), args.hyd_gra, args.OutFasta)
    else:
        print("You entered Wrong Values: ")

6:92bdc5cbf028

        OutPep = amphi_hel.sequences
        
        for i,O in enumerate(OutPep):
            OutFasta.write(">sequence_"+str(i)+'\n')
            OutFasta.write(O+'\n')


def MixedLibrary_seq(seqnum, centrosymmetric, centroasymmetric, helix, kinked, oblique, rand, randAMP, randAMPnoCM, OutFasta):

    lib = MixedLibrary(int(seqnum), int(centrosymmetric), int(centroasymmetric), int(helix), int(kinked), int(oblique), int(rand), int(randAMP), int(randAMPnoCM))
    lib.generate_sequences()
    OutFasta = open(OutFasta, 'w')

    OutPep = lib.sequences
        
    for i,O in enumerate(OutPep):
        OutFasta.write(">sequence_"+str(i)+'\n')
        OutFasta.write(O+'\n')



if __name__=='__main__':

    parser = argparse.ArgumentParser(description='Deployment tool')
    subparsers = parser.add_subparsers()

    Arc.add_argument("-m","--lenmin_s", required=False, default=7, help="")
    Arc.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max")
    Arc.add_argument("-a","--arcsize", help="Choose among 100, 140, 180, 220, 260, or choose mixed to generate a mixture")
    Arc.add_argument("-y","--hyd_gra", default='False', help="Method to mutate the generated sequences to have a hydrophobic gradient by substituting the last third of the sequence amino acids to hydrophobic.")
    Arc.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta")

    Mix = subparsers.add_parser('MixedLibrary')
    Mix.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated")
    Mix.add_argument("-c","--centrosymmetric", required=False, default=1, help="ratio of symmetric centrosymmetric sequences in the library")
    Mix.add_argument("-ca","--centroasymmetric", required=False, default=1, help="ratio of asymmetric centrosymmetric sequences in the library")
    Mix.add_argument("-hl","--helix", required=False, default=1, help="ratio of asymmetric centrosymmetric sequences in the library")
    Mix.add_argument("-k","--kinked", required=False, default=1,   help="ratio of asymmetric centrosymmetric sequences in the library")
    Mix.add_argument("-o", "--oblique", required=False, default=1,  help=" ratio of oblique oriented amphipathic helical sequences in the library")
    Mix.add_argument("-r", "--rand", required=False, default=1,  help="ratio of random sequneces in the library")
    Mix.add_argument("-ra", "--randAMP", required=False, default=1,  help="ratio of random sequences with APD2 amino acid distribution in the library")
    Mix.add_argument("-rp", "--randAMPnoCM", required=False, default=1, help="ratio of random sequences with APD2 amino acid distribution without Cys and Met in the library")
    Mix.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta")


    args = parser.parse_args()

    if sys.argv[1] == 'Random':
        Random_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.S_proba, args.OutFasta)

        Hepahelices_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.OutFasta)
    elif sys.argv[1] == 'AMPngrams':
        AMPngrams_seq(args.seq_num, args.n_min, args.n_max, args.OutFasta)
    elif sys.argv[1] == 'AmphipathicArc':
        AmphipathicArc_seq(int(args.seq_num), int(args.lenmin_s), int(args.lenmax_s), int(args.arcsize), args.hyd_gra, args.OutFasta)
    elif sys.argv[1] == 'MixedLibrary':
        MixedLibrary_seq(args.seq_num, args.centrosymmetric, args.centroasymmetric, args.helix, args.kinked, args.oblique, args.rand, args.randAMP, args.randAMPnoCM, args.OutFasta)
    else:
        print("You entered Wrong Values: ")