Mercurial > repos > proteore > proteore_venn_diagram
comparison venn_diagram.py @ 8:bca31ac678f1 draft
planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
| author | proteore |
|---|---|
| date | Fri, 28 Jun 2019 05:18:44 -0400 |
| parents | d1fd04dcb13a |
| children | e744a43171ff |
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| 7:98b7912a9ceb | 8:bca31ac678f1 |
|---|---|
| 45 title_dict[title] = name | 45 title_dict[title] = name |
| 46 ids = set() | 46 ids = set() |
| 47 if input_type == "file": | 47 if input_type == "file": |
| 48 header = inputs[i][3] | 48 header = inputs[i][3] |
| 49 ncol = inputs[i][4] | 49 ncol = inputs[i][4] |
| 50 file_content = open(input_file, "r").readlines() | 50 with open(input_file,"r") as handle : |
| 51 file_content = csv.reader(handle,delimiter="\t") | |
| 52 file_content = list(file_content) #csv object to list | |
| 51 | 53 |
| 52 # Check if column number is in right form | 54 # Check if column number is in right form |
| 53 if isnumber("int", ncol.replace("c", "")): | 55 if isnumber("int", ncol.replace("c", "")): |
| 54 if header == "true": | 56 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 | 57 file_content = [x for x in [line[int(ncol.replace("c", ""))-1].split(";") for line in file_content[1:]]] # gets ids from defined column |
| 58 else: | |
| 59 file_content = [x for x in [line[int(ncol.replace("c", ""))-1].split(";") for line in file_content]] | |
| 56 else: | 60 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 | 61 raise ValueError("Please fill in the right format of column number") |
| 58 else: | |
| 59 raise ValueError("Please fill in the right format of column number") | |
| 60 else: | 62 else: |
| 61 ids = set() | 63 ids = set() |
| 62 file_content = inputs[i][0].split() | 64 file_content = inputs[i][0].split() |
| 65 file_content = [x.split(";") for x in file_content] | |
| 63 | 66 |
| 67 file_content = [item.strip() for sublist in file_content for item in sublist if item != ''] #flat list of list of lists, remove empty items | |
| 64 ids.update(file_content) | 68 ids.update(file_content) |
| 65 if 'NA' in ids : ids.remove('NA') | 69 if 'NA' in ids : ids.remove('NA') |
| 66 comp_dict[title] = ids | 70 comp_dict[title] = ids |
| 67 | 71 |
| 68 return comp_dict, title_dict | 72 return comp_dict, title_dict |