Mercurial > repos > jay > pdaug_peptide_ngrams

comparison PDAUG_AA_Property_Based_Peptide_Generation/PDAUG_AA_Property_Based_Peptide_Generation.py @ 0:7557b48b2872 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author jay
date Wed, 28 Oct 2020 02:10:12 +0000
parents
children f5208451105a
comparison
equal deleted inserted replaced
-1:000000000000 0:7557b48b2872
1 from modlamp.sequences import *
2 import argparse, sys
3 import pandas as pd
4 import os
5
6 def Random_seq(seq_num, lenmin_s, lenmax_s, S_proba, OutFasta):
7
8 b = Random(int(seq_num), int(lenmin_s),int(lenmax_s))
9 b.generate_sequences(proba=float(S_proba))
10
11 OutPep = b.sequences
12 OutFasta = open(OutFasta, 'w')
13
14 for i,O in enumerate(OutPep):
15 OutFasta.write(">sequence_"+str(i)+'\n')
16 OutFasta.write(O+'\n')
17
18 def Helices_seq(seq_num, lenmin_s, lenmax_s, OutFasta):
19
20 h = Helices(int(seq_num), int(lenmin_s),int(lenmax_s))
21 h.generate_sequences()
22
23 OutPep = h.sequences
24 OutFasta = open(OutFasta, 'w')
25
26 for i,O in enumerate(OutPep):
27 OutFasta.write(">sequence_"+str(i)+'\n')
28 OutFasta.write(O+'\n')
29
30
31 def Kinked_seq(seq_num, lenmin_s, lenmax_s, OutFasta):
32
33 k = Kinked(int(seq_num), int(lenmin_s),int(lenmax_s))
34 k.generate_sequences()
35
36 OutPep = k.sequences
37 OutFasta = open(OutFasta, 'w')
38
39 for i,O in enumerate(OutPep):
40 OutFasta.write(">sequence_"+str(i)+'\n')
41 OutFasta.write(O+'\n')
42
43
44 def Oblique_seq(seq_num, lenmin_s, lenmax_s, OutFasta):
45
46 o = Oblique(int(seq_num), int(lenmin_s),int(lenmax_s))
47 o.generate_sequences()
48 o.sequences
49
50 OutPep = o.sequences
51 OutFasta = open(OutFasta, 'w')
52
53 for i,O in enumerate(OutPep):
54 OutFasta.write(">sequence_"+str(i)+'\n')
55 OutFasta.write(O+'\n')
56
57
58 def Centrosymmetric_seq(seq_num, lenmin_s, lenmax_s, symmetry_s, OutFasta):
59
60 s = Centrosymmetric(int(seq_num), int(lenmin_s),int(lenmax_s))
61 s.generate_sequences(symmetry=symmetry_s)
62
63 OutPep = s.sequences
64 OutFasta = open(OutFasta, 'w')
65
66 for i,O in enumerate(OutPep):
67 OutFasta.write(">sequence_"+str(i)+'\n')
68 OutFasta.write(O+'\n')
69
70
71 def HelicesACP_seq(seq_num, lenmin_s, lenmax_s, OutFasta):
72
73 helACP = HelicesACP(int(seq_num), int(lenmin_s),int(lenmax_s))
74 helACP.generate_sequences()
75
76 OutPep = helACP.sequences
77 OutFasta = open(OutFasta, 'w')
78
79 for i,O in enumerate(OutPep):
80 OutFasta.write(">sequence_"+str(i)+'\n')
81 OutFasta.write(O+'\n')
82
83
84 def Hepahelices_seq(seq_num, lenmin_s, lenmax_s, OutFasta):
85
86 h = Hepahelices(int(seq_num), int(lenmin_s),int(lenmax_s))
87 h.generate_sequences()
88
89 OutPep = h.sequences
90 OutFasta = open(OutFasta, 'w')
91
92 for i,O in enumerate(OutPep):
93 OutFasta.write(">sequence_"+str(i)+'\n')
94 OutFasta.write(O+'\n')
95
96
97 def AMPngrams_seq(seq_num, lenmin_s, lenmax_s, OutFasta):
98
99 s = AMPngrams(int(seq_num), int(lenmin_s),int(lenmax_s))
100 s.generate_sequences()
101
102 OutPep = s.sequences
103 OutFasta = open(OutFasta, 'w')
104
105 for i,O in enumerate(OutPep):
106 OutFasta.write(">sequence_"+str(i)+'\n')
107 OutFasta.write(O+'\n')
108
109 def AmphipathicArc_seq(seq_num, lenmin_s, lenmax_s, gen_seq, hyd_gra, OutFasta):
110
111 amphi_hel = AmphipathicArc(int(seq_num), int(lenmin_s),int(lenmax_s))
112 amphi_hel.generate_sequences(int(gen_seq))
113 OutFasta = open(OutFasta, 'w')
114
115 if hyd_gra == 'true':
116
117 amphi_hel.make_H_gradient()
118 OutPep = amphi_hel.sequences
119
120 for i,O in enumerate(OutPep):
121 OutFasta.write(">sequence_"+str(i)+'\n')
122 OutFasta.write(O+'\n')
123
124 elif hyd_gra == 'false':
125
126 OutPep = amphi_hel.sequences
127
128 for i,O in enumerate(OutPep):
129 OutFasta.write(">sequence_"+str(i)+'\n')
130 OutFasta.write(O+'\n')
131
132 if __name__=='__main__':
133
134 parser = argparse.ArgumentParser(description='Deployment tool')
135 subparsers = parser.add_subparsers()
136
137 Ran = subparsers.add_parser('Random')
138 Ran.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated")
139 Ran.add_argument("-m","--lenmin_s", required=False, default=7, help="")
140 Ran.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max")
141 Ran.add_argument("-p","--S_proba", required=False, default='AMP', help="AA probability to be used to generate sequences,'rand', 'AMP', 'AMPnoCM', 'randnoCM', 'ACP'")
142 Ran.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta")
143
144 Hal = subparsers.add_parser('Helices')
145 Hal.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated")
146 Hal.add_argument("-m","--lenmin_s", required=False, default=7, help="")
147 Hal.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max")
148 Hal.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta")
149
150 Kin = subparsers.add_parser('Kinked')
151 Kin.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated")
152 Kin.add_argument("-m","--lenmin_s", required=False, default=7, help="")
153 Kin.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max")
154 Kin.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta")
155
156 Obl = subparsers.add_parser('Oblique')
157 Obl.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated")
158 Obl.add_argument("-m","--lenmin_s", required=False, default=7, help="")
159 Obl.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max")
160 Obl.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta")
161
162 Cen = subparsers.add_parser('Centrosymmetric')
163 Cen.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated")
164 Cen.add_argument("-m","--lenmin_s", required=False, default=7, help="")
165 Cen.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max")
166 Cen.add_argument("-S","--symmetry_s", required=False, default="asymmetric", help="symmetric,asymmetric")
167 Cen.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta")
168
169 Hel = subparsers.add_parser('HelicesACP')
170 Hel.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated")
171 Hel.add_argument("-m","--lenmin_s", required=False, default=7, help="")
172 Hel.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max")
173 Hel.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta")
174
175 Hep = subparsers.add_parser('Hepahelices')
176 Hep.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated")
177 Hep.add_argument("-m","--lenmin_s", required=False, default=7, help="")
178 Hep.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max")
179 Hep.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta")
180
181 AMP = subparsers.add_parser('AMPngrams')
182 AMP.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated")
183 AMP.add_argument("-m","--n_min", required=False, default=3, help="minimum number of ngrams to take for sequence assembly")
184 AMP.add_argument("-M","--n_max", required=False, default=1, help="maximum number of ngrams to take for sequence assembly")
185 AMP.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta")
186
187 Arc = subparsers.add_parser('AmphipathicArc')
188 Arc.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated")
189 Arc.add_argument("-m","--lenmin_s", required=False, default=7, help="")
190 Arc.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max")
191 Arc.add_argument("-a","--arcsize", help="Choose among 100, 140, 180, 220, 260, or choose mixed to generate a mixture")
192 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.")
193 Arc.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta")
194
195 args = parser.parse_args()
196
197 if sys.argv[1] == 'Random':
198 Random_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.S_proba, args.OutFasta)
199 elif sys.argv[1] == 'Helices':
200 Helices_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.OutFasta)
201 elif sys.argv[1] == 'Kinked':
202 Kinked_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.OutFasta)
203 elif sys.argv[1] == 'Oblique':
204 Oblique_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.OutFasta)
205 elif sys.argv[1] == 'Centrosymmetric':
206 Centrosymmetric_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.symmetry_s, args.OutFasta)
207 elif sys.argv[1] == 'HelicesACP':
208 HelicesACP_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.OutFasta)
209 elif sys.argv[1] == 'Hepahelices':
210 Hepahelices_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.OutFasta)
211 elif sys.argv[1] == 'AMPngrams':
212 AMPngrams_seq(args.seq_num, args.n_min, args.n_max, args.OutFasta)
213 elif sys.argv[1] == 'AmphipathicArc':
214 AmphipathicArc_seq(int(args.seq_num), int(args.lenmin_s), int(args.lenmax_s), int(args.arcsize), args.hyd_gra, args.OutFasta)
215 else:
216 print("You entered Wrong Values: ")