Mercurial > repos > jay > pdaug_word_vector_model
view PDAUG_AA_Property_Based_Peptide_Generation/PDAUG_AA_Property_Based_Peptide_Generation.py @ 10:bc1744905ef4 draft default tip
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit d396d7ff89705cc0dd626ed32c45a9f4029b1b05"
author | jay |
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date | Wed, 12 Jan 2022 20:17:55 +0000 |
parents | e8dc2242f416 |
children |
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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') 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() 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") 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) 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) 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: ")