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comparison codon_switch.py @ 0:5397da1ef896 draft

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author gianmarco_piccinno
date Tue, 21 May 2019 05:05:15 -0400
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1 #!/usr/bin/env python
2
3 __author__= "Gianmarco Piccinno"
4 __version__ = "1.0.0"
5
6 from syngenic import *
7 from functions import *
8 from Bio import *
9 import argparse as ap
10
11 if __name__ == '__main__':
12
13 parser = ap.ArgumentParser(description="", formatter_class=ap.RawTextHelpFormatter)
14
15 parser.add_argument(
16 '-i', '--input_plasmid', help='Input plasmid', required=True)
17 parser.add_argument(
18 '-l', '--plasmid_format', help='Format of the plasmid: {fasta, genbank}', required=True)
19 parser.add_argument(
20 '-p', '--input_patterns', help='Input patterns separated by new_line', required=True)
21 parser.add_argument(
22 '-g', '--input_genome', help='Input annotated genome', required=True)
23 parser.add_argument(
24 '-q', '--genome_format', help='Format of the annotated genome: {fasta, gbk}', required=True)
25 parser.add_argument(
26 '-c', '--codon_table', help='Codon table to be used {Bacterial}', required=True)
27 parser.add_argument(
28 '-m', '--max_row', help='Max row length when print', required=False)
29 parser.add_argument(
30 '-d', '--demonstration', help='Use demonstration simplication', required=False)
31 parser.add_argument(
32 '-f', '--n_plasmids', help='Use demonstration simplication', required=False)
33 parser.add_argument(
34 '-o', '--output_folder', help='Folder for writing the output file', required=True)
35 args = vars(parser.parse_args())
36
37 """
38
39 python codon_switch_v2.py
40 -i ./pEPSA5_annotated.gb
41 -l genbank
42 -p ./patterns.txt
43 -g S_aureus_JE2.gbf
44 -q gbk -c Bacterial
45 -o ./output
46
47 python codon_switch_v2.py -i ./pEPSA5_annotated.gb -l genbank -p ./patterns.txt -g S_aureus_JE2.gbf -q genbank -c Bacterial -o ./output
48
49 """
50
51
52 pl = SeqIO.read(
53 open(args['input_plasmid'], "r"), args['plasmid_format'])
54
55 if args['demonstration'] == "demonstration":
56 pl = pl[0:3000]
57 pats = read_patterns(args['input_patterns'])
58
59
60 #############################################################
61 #
62 #############################################################
63
64 #pl = fake_from_real(path = "./data/pEPSA5_annotated.gb", id_ = "Trial", name = "Fake_plasmid")
65 print(type(pl))
66 print(pl); print(pl.seq); print(pl.features)
67
68 #for feat in pl.features:
69 # print(str(feat.extract(pl)))
70 # print(str(pl[feat.location.start:feat.location.end]))
71 # print("\n")
72
73
74 n_pl = plasmid(pl)
75 print(n_pl); print(len(n_pl))
76 print(n_pl.features)
77
78
79 patts, n_patts = all_patterns(input_ = pats)
80
81
82 f_patts = n_pl.findpatterns(n_patts, patts)
83 print(f_patts)
84 print(pl.seq)
85 print(len(pl.seq))
86
87
88 n_poss = punctuate_targets(f_patts, n_pl)
89 print(n_poss)
90
91 print_seq(n_pl.seq)
92
93 synonims_tables = synonims_(table_name=args['codon_table'])
94
95 synonims_tables
96
97 plasmids = generalization(n_poss, n_pl, synonims_tables)
98
99 print(len(plasmids))
100
101 #plasmids
102
103 #if len(plasmids) > 5000000:
104 #redo generalization without considering internal bases
105 #in target sites that are not in CDS
106 #this means considering only the outer bases of the target
107 # plasmids = generalization(n_poss, n_pl, synonims_tables,
108 # reduced = True)
109
110 #########################################################
111 # Read plasmid and compute codon usage
112 #########################################################
113
114 genome = annotated_genome(read_annotated_genome(
115 data=args['input_genome'], type_=args['genome_format']))
116
117 out_genome = genome.codon_usage(args['codon_table'])
118 print(out_genome.keys())
119 print(out_genome["Table"])
120
121 print(out_genome["Table"].loc["GCA"]["Proportion"])
122 print(type(out_genome["Table"].loc["GCA"]["Proportion"]))
123
124
125 #########################################################
126 # Evaluate the plasmid
127 #########################################################
128
129 useful_plasmids = evaluate_plasmids(plasmids = plasmids,
130 original_plasmid = n_pl,
131 codon_usage_table = out_genome["Table"],
132 n_patts = n_patts,
133 f_patts = patts)
134
135 dat_plasmids = rank_plasmids(original_useful_plasmids = useful_plasmids)
136
137 def_pls = dat_plasmids.index[:int(args['n_plasmids'])]
138
139 for to_save in def_pls:
140 #print(to_save)
141 #print(useful_plasmids[to_save])
142 with open(to_save+".fa", "w") as handle:
143 handle.write(">"+to_save+"\n")
144 handle.write(useful_plasmids[to_save]["sequence"])
145
146
147
148 if args['max_row'] != None:
149 tmp_max_row = int(args['max_row'])
150 else:
151 tmp_max_row = 27
152
153 print_color_seq(original = n_pl,
154 others = def_pls,
155 annotation_information = useful_plasmids,
156 tot = useful_plasmids,
157 ind_range = None,
158 patterns = n_poss,
159 f_patterns = f_patts,
160 patts = patts,
161 max_row = tmp_max_row)
162
163
164 print_to_pdf(original = n_pl,
165 others = def_pls,
166 annotation_information = useful_plasmids,
167 tot = useful_plasmids,
168 ind_range = None,
169 patterns = n_poss,
170 f_patterns = f_patts,
171 patts = patts,
172 max_row = tmp_max_row)