Mercurial > repos > proteore > proteore_venn_diagram
comparison venn_diagram.py @ 3:145f347dc0e1 draft
planemo upload commit b5beb4f7f3c60838b88a4cc32dfcb94c399d20ce-dirty
| author | proteore |
|---|---|
| date | Tue, 20 Mar 2018 06:35:27 -0400 |
| parents | 9d4f20618ab4 |
| children | d1fd04dcb13a |
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| 2:774d9cbe6937 | 3:145f347dc0e1 |
|---|---|
| 16 | 16 |
| 17 def isnumber(format, n): | 17 def isnumber(format, n): |
| 18 """ | 18 """ |
| 19 Check if an element is integer or float | 19 Check if an element is integer or float |
| 20 """ | 20 """ |
| 21 float_format = re.compile("^[\-]?[1-9][0-9]*\.?[0-9]+$") | 21 float_format = re.compile(r"^[-]?[1-9][0-9]*.?[0-9]+$") |
| 22 int_format = re.compile("^[\-]?[1-9][0-9]*$") | 22 int_format = re.compile(r"^[-]?[1-9][0-9]*$") |
| 23 test = "" | 23 test = "" |
| 24 if format == "int": | 24 if format == "int": |
| 25 test = re.match(int_format, n) | 25 test = re.match(int_format, n) |
| 26 elif format == "float": | 26 elif format == "float": |
| 27 test = re.match(float_format, n) | 27 test = re.match(float_format, n) |
| 53 if isnumber("int", ncol.replace("c", "")): | 53 if isnumber("int", ncol.replace("c", "")): |
| 54 if header == "true": | 54 if header == "true": |
| 55 file_content = [x.strip() for x in [line.split("\t")[int(ncol.replace("c", ""))-1].split(";")[0] for line in file_content[1:]]] # take only first IDs | 55 file_content = [x.strip() for x in [line.split("\t")[int(ncol.replace("c", ""))-1].split(";")[0] for line in file_content[1:]]] # take only first IDs |
| 56 else: | 56 else: |
| 57 file_content = [x.strip() for x in [line.split("\t")[int(ncol.replace("c", ""))-1].split(";")[0] for line in file_content]] # take only first IDs | 57 file_content = [x.strip() for x in [line.split("\t")[int(ncol.replace("c", ""))-1].split(";")[0] for line in file_content]] # take only first IDs |
| 58 #print(file_content[1:13]) | |
| 59 else: | 58 else: |
| 60 raise ValueError("Please fill in the right format of column number") | 59 raise ValueError("Please fill in the right format of column number") |
| 61 else: | 60 else: |
| 62 ids = set() | 61 ids = set() |
| 63 file_content = inputs[i][0].split() | 62 file_content = inputs[i][0].split() |
| 76 for group in combinations(sorted(comp_dict), i): | 75 for group in combinations(sorted(comp_dict), i): |
| 77 others = set() | 76 others = set() |
| 78 [others.add(name) for name in names if name not in group] | 77 [others.add(name) for name in names if name not in group] |
| 79 difference = [] | 78 difference = [] |
| 80 intersected = set.intersection(*(comp_dict[k] for k in group)) | 79 intersected = set.intersection(*(comp_dict[k] for k in group)) |
| 81 n = "".join(group) | |
| 82 if len(others) > 0: | 80 if len(others) > 0: |
| 83 difference = intersected.difference(set.union(*(comp_dict[k] for k in others))) | 81 difference = intersected.difference(set.union(*(comp_dict[k] for k in others))) |
| 84 yield group, list(intersected), list(difference) | 82 yield group, list(intersected), list(difference) |
| 85 | 83 |
| 86 def diagram(comp_dict, title_dict): | 84 def diagram(comp_dict, title_dict): |
| 113 """ | 111 """ |
| 114 output = open("venn_diagram_text_output.txt", "w") | 112 output = open("venn_diagram_text_output.txt", "w") |
| 115 string = "" | 113 string = "" |
| 116 lines = [] | 114 lines = [] |
| 117 result = dict((k, v) for k, v in json_result["data"].iteritems() if v != []) | 115 result = dict((k, v) for k, v in json_result["data"].iteritems() if v != []) |
| 118 print(result) | |
| 119 max_count = max(len(v) for v in result.values()) | 116 max_count = max(len(v) for v in result.values()) |
| 120 print(max_count) | |
| 121 for i in range(max_count): | 117 for i in range(max_count): |
| 122 lines.append("") | 118 lines.append("") |
| 123 | 119 |
| 124 for i in range(max_count): | 120 for i in range(max_count): |
| 125 header = "" | 121 header = "" |
| 126 for d in range(len(result.keys())): | 122 for d in range(len(result.keys())): |
| 127 data = result.keys()[d] | 123 data = result.keys()[d] |
| 128 name = "_".join([json_result["name"][x] for x in data]) | 124 name = "_".join([json_result["name"][x] for x in data]) |
| 129 header += name + "\t" | 125 header += name + "\t" |
| 130 if len(result[data]) > i: | 126 if len(result[data]) > i: |
| 127 print("a", result[data][i]) | |
| 131 lines[i] += result[data][i] + "\t" | 128 lines[i] += result[data][i] + "\t" |
| 132 else: | 129 else: |
| 133 lines[i] += "\t" | 130 lines[i] += "\t" |
| 131 # Strip last tab in the end of the lines | |
| 132 header = header.rstrip() | |
| 133 lines = [line.rstrip() for line in lines] | |
| 134 string += header + "\n" | 134 string += header + "\n" |
| 135 string += "\n".join(lines) | 135 string += "\n".join(lines) |
| 136 print(string) | |
| 137 output.write(string) | 136 output.write(string) |
| 138 output.close() | 137 output.close() |
| 139 | 138 |
| 140 def write_summary( summary_file, inputs): | 139 def write_summary(summary_file, inputs): |
| 141 """ | 140 """ |
| 142 Paste json string into template file | 141 Paste json string into template file |
| 143 """ | 142 """ |
| 144 a, b = input_to_dict(inputs) | 143 a, b = input_to_dict(inputs) |
| 145 data = diagram(a, b) | 144 data = diagram(a, b) |