Mercurial > repos > iuc > vsnp_get_snps

comparison vsnp_determine_ref_from_data.py @ 0:ec6e02f4eab7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
author iuc
date Tue, 16 Nov 2021 08:26:58 +0000
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-1:000000000000 0:ec6e02f4eab7
1 #!/usr/bin/env python
2
3 import argparse
4 import gzip
5 import os
6 from collections import OrderedDict
7
8 import yaml
9 from Bio.SeqIO.QualityIO import FastqGeneralIterator
10
11 OUTPUT_DBKEY_DIR = 'output_dbkey'
12 OUTPUT_METRICS_DIR = 'output_metrics'
13
14
15 def get_sample_name(file_path):
16 base_file_name = os.path.basename(file_path)
17 if base_file_name.find(".") > 0:
18 # Eliminate the extension.
19 return os.path.splitext(base_file_name)[0]
20 return base_file_name
21
22
23 def get_dbkey(dnaprints_dict, key, s):
24 # dnaprints_dict looks something like this:
25 # {'brucella': {'NC_002945v4': ['11001110', '11011110', '11001100']}
26 # {'bovis': {'NC_006895': ['11111110', '00010010', '01111011']}}
27 d = dnaprints_dict.get(key, {})
28 for data_table_value, v_list in d.items():
29 if s in v_list:
30 return data_table_value
31 return ""
32
33
34 def get_dnaprints_dict(dnaprint_fields):
35 # A dndprint_fields entry looks something liek this.
36 # [['AF2122', '/galaxy/tool-data/vsnp/AF2122/dnaprints/NC_002945v4.yml']]
37 dnaprints_dict = {}
38 for item in dnaprint_fields:
39 # Here item is a 2-element list of data
40 # table components, # value and path.
41 value = item[0]
42 path = item[1].strip()
43 with open(path, "rt") as fh:
44 # The format of all dnaprints yaml
45 # files is something like this:
46 # brucella:
47 # - 0111111111111111
48 print_dict = yaml.load(fh, Loader=yaml.Loader)
49 for print_dict_k, print_dict_v in print_dict.items():
50 dnaprints_v_dict = dnaprints_dict.get(print_dict_k, {})
51 if len(dnaprints_v_dict) > 0:
52 # dnaprints_dict already contains k (e.g., 'brucella',
53 # and dnaprints_v_dict will be a dictionary # that
54 # looks something like this:
55 # {'NC_002945v4': ['11001110', '11011110', '11001100']}
56 value_list = dnaprints_v_dict.get(value, [])
57 value_list = value_list + print_dict_v
58 dnaprints_v_dict[value] = value_list
59 else:
60 # dnaprints_v_dict is an empty dictionary.
61 dnaprints_v_dict[value] = print_dict_v
62 dnaprints_dict[print_dict_k] = dnaprints_v_dict
63 # dnaprints_dict looks something like this:
64 # {'brucella': {'NC_002945v4': ['11001110', '11011110', '11001100']}
65 # {'bovis': {'NC_006895': ['11111110', '00010010', '01111011']}}
66 return dnaprints_dict
67
68
69 def get_group_and_dbkey(dnaprints_dict, brucella_string, brucella_sum, bovis_string, bovis_sum, para_string, para_sum):
70 if brucella_sum > 3:
71 group = "Brucella"
72 dbkey = get_dbkey(dnaprints_dict, "brucella", brucella_string)
73 elif bovis_sum > 3:
74 group = "TB"
75 dbkey = get_dbkey(dnaprints_dict, "bovis", bovis_string)
76 elif para_sum >= 1:
77 group = "paraTB"
78 dbkey = get_dbkey(dnaprints_dict, "para", para_string)
79 else:
80 group = ""
81 dbkey = ""
82 return group, dbkey
83
84
85 def get_oligo_dict():
86 oligo_dict = {}
87 oligo_dict["01_ab1"] = "AATTGTCGGATAGCCTGGCGATAACGACGC"
88 oligo_dict["02_ab3"] = "CACACGCGGGCCGGAACTGCCGCAAATGAC"
89 oligo_dict["03_ab5"] = "GCTGAAGCGGCAGACCGGCAGAACGAATAT"
90 oligo_dict["04_mel"] = "TGTCGCGCGTCAAGCGGCGTGAAATCTCTG"
91 oligo_dict["05_suis1"] = "TGCGTTGCCGTGAAGCTTAATTCGGCTGAT"
92 oligo_dict["06_suis2"] = "GGCAATCATGCGCAGGGCTTTGCATTCGTC"
93 oligo_dict["07_suis3"] = "CAAGGCAGATGCACATAATCCGGCGACCCG"
94 oligo_dict["08_ceti1"] = "GTGAATATAGGGTGAATTGATCTTCAGCCG"
95 oligo_dict["09_ceti2"] = "TTACAAGCAGGCCTATGAGCGCGGCGTGAA"
96 oligo_dict["10_canis4"] = "CTGCTACATAAAGCACCCGGCGACCGAGTT"
97 oligo_dict["11_canis"] = "ATCGTTTTGCGGCATATCGCTGACCACAGC"
98 oligo_dict["12_ovis"] = "CACTCAATCTTCTCTACGGGCGTGGTATCC"
99 oligo_dict["13_ether2"] = "CGAAATCGTGGTGAAGGACGGGACCGAACC"
100 oligo_dict["14_63B1"] = "CCTGTTTAAAAGAATCGTCGGAACCGCTCT"
101 oligo_dict["15_16M0"] = "TCCCGCCGCCATGCCGCCGAAAGTCGCCGT"
102 oligo_dict["16_mel1b"] = "TCTGTCCAAACCCCGTGACCGAACAATAGA"
103 oligo_dict["17_tb157"] = "CTCTTCGTATACCGTTCCGTCGTCACCATGGTCCT"
104 oligo_dict["18_tb7"] = "TCACGCAGCCAACGATATTCGTGTACCGCGACGGT"
105 oligo_dict["19_tbbov"] = "CTGGGCGACCCGGCCGACCTGCACACCGCGCATCA"
106 oligo_dict["20_tb5"] = "CCGTGGTGGCGTATCGGGCCCCTGGATCGCGCCCT"
107 oligo_dict["21_tb2"] = "ATGTCTGCGTAAAGAAGTTCCATGTCCGGGAAGTA"
108 oligo_dict["22_tb3"] = "GAAGACCTTGATGCCGATCTGGGTGTCGATCTTGA"
109 oligo_dict["23_tb4"] = "CGGTGTTGAAGGGTCCCCCGTTCCAGAAGCCGGTG"
110 oligo_dict["24_tb6"] = "ACGGTGATTCGGGTGGTCGACACCGATGGTTCAGA"
111 oligo_dict["25_para"] = "CCTTTCTTGAAGGGTGTTCG"
112 oligo_dict["26_para_sheep"] = "CGTGGTGGCGACGGCGGCGGGCCTGTCTAT"
113 oligo_dict["27_para_cattle"] = "TCTCCTCGGTCGGTGATTCGGGGGCGCGGT"
114 return oligo_dict
115
116
117 def get_seq_counts(value, fastq_list, gzipped):
118 count = 0
119 for fastq_file in fastq_list:
120 if gzipped:
121 with gzip.open(fastq_file, 'rt') as fh:
122 for title, seq, qual in FastqGeneralIterator(fh):
123 count += seq.count(value)
124 else:
125 with open(fastq_file, 'r') as fh:
126 for title, seq, qual in FastqGeneralIterator(fh):
127 count += seq.count(value)
128 return(value, count)
129
130
131 def get_species_counts(fastq_list, gzipped):
132 count_summary = {}
133 oligo_dict = get_oligo_dict()
134 for v1 in oligo_dict.values():
135 returned_value, count = get_seq_counts(v1, fastq_list, gzipped)
136 for key, v2 in oligo_dict.items():
137 if returned_value == v2:
138 count_summary.update({key: count})
139 count_list = []
140 for v in count_summary.values():
141 count_list.append(v)
142 brucella_sum = sum(count_list[:16])
143 bovis_sum = sum(count_list[16:24])
144 para_sum = sum(count_list[24:])
145 return count_summary, count_list, brucella_sum, bovis_sum, para_sum
146
147
148 def get_species_strings(count_summary):
149 binary_dictionary = {}
150 for k, v in count_summary.items():
151 if v > 1:
152 binary_dictionary.update({k: 1})
153 else:
154 binary_dictionary.update({k: 0})
155 binary_dictionary = OrderedDict(sorted(binary_dictionary.items()))
156 binary_list = []
157 for v in binary_dictionary.values():
158 binary_list.append(v)
159 brucella_binary = binary_list[:16]
160 brucella_string = ''.join(str(e) for e in brucella_binary)
161 bovis_binary = binary_list[16:24]
162 bovis_string = ''.join(str(e) for e in bovis_binary)
163 para_binary = binary_list[24:]
164 para_string = ''.join(str(e) for e in para_binary)
165 return brucella_string, bovis_string, para_string
166
167
168 def output_dbkey(file_name, dbkey, output_file):
169 # Output the dbkey.
170 with open(output_file, "w") as fh:
171 fh.write("%s" % dbkey)
172
173
174 def output_files(fastq_file, count_list, group, dbkey, dbkey_file, metrics_file):
175 base_file_name = get_sample_name(fastq_file)
176 output_dbkey(base_file_name, dbkey, dbkey_file)
177 output_metrics(base_file_name, count_list, group, dbkey, metrics_file)
178
179
180 def output_metrics(file_name, count_list, group, dbkey, output_file):
181 # Output the metrics.
182 with open(output_file, "w") as fh:
183 fh.write("Sample: %s\n" % file_name)
184 fh.write("Brucella counts: ")
185 for i in count_list[:16]:
186 fh.write("%d," % i)
187 fh.write("\nTB counts: ")
188 for i in count_list[16:24]:
189 fh.write("%d," % i)
190 fh.write("\nPara counts: ")
191 for i in count_list[24:]:
192 fh.write("%d," % i)
193 fh.write("\nGroup: %s" % group)
194 fh.write("\ndbkey: %s\n" % dbkey)
195
196
197 if __name__ == '__main__':
198 parser = argparse.ArgumentParser()
199
200 parser.add_argument('--dnaprint_fields', action='append', dest='dnaprint_fields', nargs=2, help="List of dnaprints data table value, name and path fields")
201 parser.add_argument('--read1', action='store', dest='read1', help='Required: single read')
202 parser.add_argument('--read2', action='store', dest='read2', required=False, default=None, help='Optional: paired read')
203 parser.add_argument('--gzipped', action='store_true', dest='gzipped', help='Input files are gzipped')
204 parser.add_argument('--output_dbkey', action='store', dest='output_dbkey', help='Output reference file')
205 parser.add_argument('--output_metrics', action='store', dest='output_metrics', help='Output metrics file')
206
207 args = parser.parse_args()
208
209 fastq_list = [args.read1]
210 if args.read2 is not None:
211 fastq_list.append(args.read2)
212
213 # The value of dnaprint_fields is a list of lists, where each list is
214 # the [value, name, path] components of the vsnp_dnaprints data table.
215 # The data_manager_vsnp_dnaprints tool assigns the dbkey column from the
216 # all_fasta data table to the value column in the vsnp_dnaprints data
217 # table to ensure a proper mapping for discovering the dbkey.
218 dnaprints_dict = get_dnaprints_dict(args.dnaprint_fields)
219
220 # Here fastq_list consists of either a single read
221 # or a set of paired reads, producing single outputs.
222 count_summary, count_list, brucella_sum, bovis_sum, para_sum = get_species_counts(fastq_list, args.gzipped)
223 brucella_string, bovis_string, para_string = get_species_strings(count_summary)
224 group, dbkey = get_group_and_dbkey(dnaprints_dict, brucella_string, brucella_sum, bovis_string, bovis_sum, para_string, para_sum)
225 output_files(args.read1, count_list, group, dbkey, dbkey_file=args.output_dbkey, metrics_file=args.output_metrics)