Mercurial > repos > jay > pdaug_word_vector_model
diff PDAUG_AA_Property_Based_Peptide_Generation/PDAUG_AA_Property_Based_Peptide_Generation.py @ 0:3ce435b8d648 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author | jay |
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date | Wed, 28 Oct 2020 02:21:16 +0000 |
parents | |
children | e8dc2242f416 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_AA_Property_Based_Peptide_Generation/PDAUG_AA_Property_Based_Peptide_Generation.py Wed Oct 28 02:21:16 2020 +0000 @@ -0,0 +1,216 @@ +from modlamp.sequences import * +import argparse, sys +import pandas as pd +import os + +def Random_seq(seq_num, lenmin_s, lenmax_s, S_proba, OutFasta): + + b = Random(int(seq_num), int(lenmin_s),int(lenmax_s)) + b.generate_sequences(proba=float(S_proba)) + + OutPep = b.sequences + OutFasta = open(OutFasta, 'w') + + for i,O in enumerate(OutPep): + OutFasta.write(">sequence_"+str(i)+'\n') + OutFasta.write(O+'\n') + +def Helices_seq(seq_num, lenmin_s, lenmax_s, OutFasta): + + h = Helices(int(seq_num), int(lenmin_s),int(lenmax_s)) + h.generate_sequences() + + OutPep = h.sequences + OutFasta = open(OutFasta, 'w') + + for i,O in enumerate(OutPep): + OutFasta.write(">sequence_"+str(i)+'\n') + OutFasta.write(O+'\n') + + +def Kinked_seq(seq_num, lenmin_s, lenmax_s, OutFasta): + + k = Kinked(int(seq_num), int(lenmin_s),int(lenmax_s)) + k.generate_sequences() + + OutPep = k.sequences + OutFasta = open(OutFasta, 'w') + + for i,O in enumerate(OutPep): + OutFasta.write(">sequence_"+str(i)+'\n') + OutFasta.write(O+'\n') + + +def Oblique_seq(seq_num, lenmin_s, lenmax_s, OutFasta): + + o = Oblique(int(seq_num), int(lenmin_s),int(lenmax_s)) + o.generate_sequences() + o.sequences + + OutPep = o.sequences + OutFasta = open(OutFasta, 'w') + + for i,O in enumerate(OutPep): + OutFasta.write(">sequence_"+str(i)+'\n') + OutFasta.write(O+'\n') + + +def Centrosymmetric_seq(seq_num, lenmin_s, lenmax_s, symmetry_s, OutFasta): + + s = Centrosymmetric(int(seq_num), int(lenmin_s),int(lenmax_s)) + s.generate_sequences(symmetry=symmetry_s) + + OutPep = s.sequences + OutFasta = open(OutFasta, 'w') + + for i,O in enumerate(OutPep): + OutFasta.write(">sequence_"+str(i)+'\n') + OutFasta.write(O+'\n') + + +def HelicesACP_seq(seq_num, lenmin_s, lenmax_s, OutFasta): + + helACP = HelicesACP(int(seq_num), int(lenmin_s),int(lenmax_s)) + helACP.generate_sequences() + + OutPep = helACP.sequences + OutFasta = open(OutFasta, 'w') + + for i,O in enumerate(OutPep): + OutFasta.write(">sequence_"+str(i)+'\n') + OutFasta.write(O+'\n') + + +def Hepahelices_seq(seq_num, lenmin_s, lenmax_s, OutFasta): + + h = Hepahelices(int(seq_num), int(lenmin_s),int(lenmax_s)) + h.generate_sequences() + + OutPep = h.sequences + OutFasta = open(OutFasta, 'w') + + for i,O in enumerate(OutPep): + OutFasta.write(">sequence_"+str(i)+'\n') + OutFasta.write(O+'\n') + + +def AMPngrams_seq(seq_num, lenmin_s, lenmax_s, OutFasta): + + s = AMPngrams(int(seq_num), int(lenmin_s),int(lenmax_s)) + s.generate_sequences() + + OutPep = s.sequences + OutFasta = open(OutFasta, 'w') + + for i,O in enumerate(OutPep): + OutFasta.write(">sequence_"+str(i)+'\n') + OutFasta.write(O+'\n') + +def AmphipathicArc_seq(seq_num, lenmin_s, lenmax_s, gen_seq, hyd_gra, OutFasta): + + amphi_hel = AmphipathicArc(int(seq_num), int(lenmin_s),int(lenmax_s)) + amphi_hel.generate_sequences(int(gen_seq)) + OutFasta = open(OutFasta, 'w') + + if hyd_gra == 'true': + + amphi_hel.make_H_gradient() + OutPep = amphi_hel.sequences + + for i,O in enumerate(OutPep): + OutFasta.write(">sequence_"+str(i)+'\n') + OutFasta.write(O+'\n') + + elif hyd_gra == 'false': + + 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() + + Ran = subparsers.add_parser('Random') + Ran.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated") + Ran.add_argument("-m","--lenmin_s", required=False, default=7, help="") + Ran.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max") + Ran.add_argument("-p","--S_proba", required=False, default='AMP', help="AA probability to be used to generate sequences,'rand', 'AMP', 'AMPnoCM', 'randnoCM', 'ACP'") + Ran.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta") + + Hal = subparsers.add_parser('Helices') + Hal.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated") + Hal.add_argument("-m","--lenmin_s", required=False, default=7, help="") + Hal.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max") + Hal.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta") + + Kin = subparsers.add_parser('Kinked') + Kin.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated") + Kin.add_argument("-m","--lenmin_s", required=False, default=7, help="") + Kin.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max") + Kin.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta") + + Obl = subparsers.add_parser('Oblique') + Obl.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated") + Obl.add_argument("-m","--lenmin_s", required=False, default=7, help="") + Obl.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max") + Obl.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta") + + Cen = subparsers.add_parser('Centrosymmetric') + Cen.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated") + Cen.add_argument("-m","--lenmin_s", required=False, default=7, help="") + Cen.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max") + Cen.add_argument("-S","--symmetry_s", required=False, default="asymmetric", help="symmetric,asymmetric") + Cen.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta") + + Hel = subparsers.add_parser('HelicesACP') + Hel.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated") + Hel.add_argument("-m","--lenmin_s", required=False, default=7, help="") + Hel.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max") + Hel.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta") + + Hep = subparsers.add_parser('Hepahelices') + Hep.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated") + Hep.add_argument("-m","--lenmin_s", required=False, default=7, help="") + Hep.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max") + Hep.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta") + + AMP = subparsers.add_parser('AMPngrams') + AMP.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated") + AMP.add_argument("-m","--n_min", required=False, default=3, help="minimum number of ngrams to take for sequence assembly") + AMP.add_argument("-M","--n_max", required=False, default=1, help="maximum number of ngrams to take for sequence assembly") + AMP.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta") + + Arc = subparsers.add_parser('AmphipathicArc') + Arc.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated") + 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) + elif sys.argv[1] == 'Helices': + Helices_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.OutFasta) + elif sys.argv[1] == 'Kinked': + Kinked_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.OutFasta) + elif sys.argv[1] == 'Oblique': + Oblique_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.OutFasta) + elif sys.argv[1] == 'Centrosymmetric': + Centrosymmetric_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.symmetry_s, args.OutFasta) + elif sys.argv[1] == 'HelicesACP': + HelicesACP_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.OutFasta) + elif sys.argv[1] == 'Hepahelices': + 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: ") \ No newline at end of file