Mercurial > repos > galaxyp > proteore_venn_diagram

comparison venn_diagram.py @ 0:57f01ca855cd draft default tip

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"planemo upload commit 47d779aa1de5153673ac8bb1e37c9730210cbb5d"
author galaxyp
date Sat, 12 Jun 2021 18:06:28 +0000
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-1:000000000000 0:57f01ca855cd
1 #!/usr/bin/env python
2
3 import argparse
4 import csv
5 import json
6 import os
7 import re
8 from itertools import combinations
9
10
11 CURRENT_DIR = os.path.dirname(os.path.abspath(__file__))
12
13 ########################################################################
14 # FUNCTIONS
15 ########################################################################
16
17
18 def isnumber(format, n):
19 """
20 Check if an element is integer or float
21 """
22 float_format = re.compile(r"^[-]?[1-9][0-9]*.?[0-9]+$")
23 int_format = re.compile(r"^[-]?[1-9][0-9]*$")
24 test = ""
25 if format == "int":
26 test = re.match(int_format, n)
27 elif format == "float":
28 test = re.match(float_format, n)
29 if test:
30 return True
31 else:
32 return False
33
34
35 def input_to_dict(inputs):
36 """
37 Parse input and return a dictionary of name and data of each lists/files
38 """
39 comp_dict = {}
40 title_dict = {}
41 c = ["A", "B", "C", "D", "E", "F"]
42 for i in range(len(inputs)):
43 input_file = inputs[i][0]
44 name = inputs[i][1]
45 input_type = inputs[i][2]
46 title = c[i]
47 title_dict[title] = name
48 ids = set()
49 if input_type == "file":
50 header = inputs[i][3]
51 ncol = inputs[i][4]
52 with open(input_file, "r") as handle:
53 file_content = csv.reader(handle, delimiter="\t")
54 file_content = list(file_content) # csv object to list
55
56 # Check if column number is in right form
57 if isnumber("int", ncol.replace("c", "")):
58 if header == "true":
59 # gets ids from defined column
60 file_content = [x for x in [line[int(ncol.replace("c", ""))-1].split(";") for line in file_content[1:]]] # noqa 501
61
62 else:
63 file_content = [x for x in [line[int(ncol.replace("c", ""))-1].split(";") for line in file_content]] # noqa 501
64 else:
65 raise ValueError("Please fill in the right format of column number") # noqa 501
66 else:
67 ids = set()
68 file_content = inputs[i][0].split()
69 file_content = [x.split(";") for x in file_content]
70
71 # flat list of list of lists, remove empty items
72 file_content = [item.strip() for sublist in file_content for item in sublist if item != ''] # noqa 501
73 ids.update(file_content)
74 if 'NA' in ids:
75 ids.remove('NA')
76 comp_dict[title] = ids
77
78 return comp_dict, title_dict
79
80
81 def intersect(comp_dict):
82 """
83 Calculate the intersections of input
84 """
85 names = set(comp_dict)
86 for i in range(1, len(comp_dict) + 1):
87 for group in combinations(sorted(comp_dict), i):
88 others = set()
89 [others.add(name) for name in names if name not in group]
90 difference = []
91 intersected = set.intersection(*(comp_dict[k] for k in group))
92 if len(others) > 0:
93 difference = intersected.difference(set.union(*(comp_dict[k] for k in others))) # noqa 501
94 yield group, list(intersected), list(difference)
95
96
97 def diagram(comp_dict, title_dict):
98 """
99 Create json string for jvenn diagram plot
100 """
101 result = {}
102 result["name"] = {}
103 for k in comp_dict.keys():
104 result["name"][k] = title_dict[k]
105
106 result["data"] = {}
107 result["values"] = {}
108 for group, intersected, difference in intersect(comp_dict):
109 if len(group) == 1:
110 result["data"]["".join(group)] = sorted(difference)
111 result["values"]["".join(group)] = len(difference)
112 elif len(group) > 1 and len(group) < len(comp_dict):
113 result["data"]["".join(group)] = sorted(difference)
114 result["values"]["".join(group)] = len(difference)
115 elif len(group) == len(comp_dict):
116 result["data"]["".join(group)] = sorted(intersected)
117 result["values"]["".join(group)] = len(intersected)
118
119 return result
120
121 # Write intersections of input to text output file
122
123
124 def write_text_venn(json_result):
125 lines = []
126 result = dict((k, v) for k, v in json_result["data"].items() if v != []) # noqa 501
127 for key in result:
128 if 'NA' in result[key]:
129 result[key].remove("NA")
130
131 list_names = dict((k, v) for k, v in json_result["name"].items() if v != []) # noqa 501
132 nb_lines_max = max(len(v) for v in result.values())
133
134 # get list names associated to each column
135 column_dict = {}
136 for key in result:
137 if key in list_names:
138 column_dict[key] = list_names[key]
139 else:
140 keys = list(key)
141 column_dict[key] = "_".join([list_names[k] for k in keys])
142
143 # construct tsv
144 for key in result:
145 line = result[key]
146 if len(line) < nb_lines_max:
147 line.extend([''] * (nb_lines_max - len(line)))
148 line = [column_dict[key]] + line # add header
149 lines.append(line)
150 # transpose tsv
151 lines = zip(*lines)
152
153 with open("venn_diagram_text_output.tsv", "w") as output:
154 tsv_output = csv.writer(output, delimiter='\t')
155 tsv_output.writerows(lines)
156
157
158 def write_summary(summary_file, inputs):
159 """
160 Paste json string into template file
161 """
162 a, b = input_to_dict(inputs)
163 data = diagram(a, b)
164 write_text_venn(data)
165
166 to_replace = {
167 "series": [data],
168 "displayStat": "true",
169 "displaySwitch": "true",
170 "shortNumber": "true",
171 }
172
173 FH_summary_tpl = open(os.path.join(CURRENT_DIR, "jvenn_template.html"))
174 FH_summary_out = open(summary_file, "w")
175 for line in FH_summary_tpl:
176 if "###JVENN_DATA###" in line:
177 line = line.replace("###JVENN_DATA###", json.dumps(to_replace))
178 FH_summary_out.write(line)
179
180 FH_summary_out.close()
181 FH_summary_tpl.close()
182
183
184 def process(args):
185 write_summary(args.summary, args.input)
186
187
188 #####################################################################
189 # MAIN
190 #####################################################################
191 if __name__ == '__main__':
192 # Parse parameters
193 parser = argparse.ArgumentParser(description='Filters an abundance file')
194 group_input = parser.add_argument_group('Inputs')
195 group_input.add_argument('--input', nargs="+", action="append",
196 required=True, help="The input tabular file.")
197 group_output = parser.add_argument_group('Outputs')
198 group_output.add_argument('--summary', default="summary.html",
199 help="The HTML file containing the graphs. \
200 [Default: %(default)s]")
201 args = parser.parse_args()
202
203 # Process
204 process(args)