Mercurial > repos > iuc > ena_upload

annotate process_xlsx.py @ 2:9e2df763086c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
author iuc
date Thu, 15 Jul 2021 20:12:34 +0000
parents 57251c760cab
children 59bb6d34fca6
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382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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diff changeset
1 import argparse
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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2 import pathlib
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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3 import sys
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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4
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5 import xlrd
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6 import yaml
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7 from mappings import optional_samples_cols_mapping
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8
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9 FILE_FORMAT = 'fastq'
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11
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12 def extract_data(xl_sheet, expected_columns, optional_cols=None):
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13 """
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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14 1. Check that the columns I expect are present in the sheet
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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15 (any order and mixed with others, it's just a verification that
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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16 the user filled the correct template)
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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17 2. Fill a dictionary with the rows data indexed by first column in list"""
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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18 sheet_columns = {}
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19 if optional_cols is None:
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20 optional_cols = []
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
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21 optional_cols_loaded = []
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22 for sh_col in range(xl_sheet.ncols):
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23 if (xl_sheet.cell(0, sh_col).value in expected_columns) \
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
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24 or (xl_sheet.cell(0, sh_col).value in optional_cols):
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382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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25 if xl_sheet.cell(0, sh_col).value in sheet_columns.keys():
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26 sys.exit("Duplicated columns found")
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27 else:
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28 sheet_columns[xl_sheet.cell(0, sh_col).value] = sh_col
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29 if xl_sheet.cell(0, sh_col).value in optional_cols:
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
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30 # store the list of optional cols available
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
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31 optional_cols_loaded.append(xl_sheet.cell(0, sh_col).value)
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
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32 provided_cols = expected_columns + optional_cols_loaded
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33
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34 # check that the required columns are all present
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
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35 # TODO: revise this for optional columns
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36 for col in range(len(expected_columns)):
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37 assert expected_columns[col] in sheet_columns.keys(), \
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38 "Expected column %s not found" % expected_columns[col]
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39
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40 # fetch rows in a dict
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41 data_dict = {}
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42 # the first of the expected columns will be the index
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43 index_col = sheet_columns[expected_columns[0]]
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44 # skip first 2 rows: column names + comments rows
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45 for row_id in range(2, xl_sheet.nrows):
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46 row_dict = {}
2
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47 for col in range(1, len(provided_cols)):
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48 sheet_col_index = sheet_columns[provided_cols[col]]
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49 row_dict[provided_cols[col]] = xl_sheet.cell(row_id, sheet_col_index).value
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50 # should check for duplicate alias/ids?
1
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51 if xl_sheet.cell(row_id, index_col).value in data_dict.keys():
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52 tmp = data_dict[xl_sheet.cell(row_id, index_col).value]
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53 data_dict[xl_sheet.cell(row_id, index_col).value] = [tmp]
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54 data_dict[xl_sheet.cell(row_id, index_col).value].append(row_dict)
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55 else:
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56 data_dict[xl_sheet.cell(row_id, index_col).value] = row_dict
2
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57 return data_dict, optional_cols_loaded
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58
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59
1
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60 def paste_xls2yaml(xlsx_path):
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61 print('YAML -------------')
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62 xls = xlrd.open_workbook(xlsx_path)
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63 content_dict = {}
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64 for sheet_name in xls.sheet_names():
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65 if sheet_name == 'controlled_vocabulary':
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66 continue
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67 xls_sheet = xls.sheet_by_name(sheet_name)
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68 sheet_contents_dict = {}
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69 colnames = []
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70 for col in range(xls_sheet.ncols):
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71 colnames.append(xls_sheet.cell(0, col).value)
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72 # skip first 2 rows (column names and suggestions)
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73 for row_id in range(2, xls_sheet.nrows):
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74 row_dict = {}
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75 for col_id in range(0, xls_sheet.ncols):
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76 row_dict[colnames[col_id]] = xls_sheet.cell(row_id, col_id).value
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77 # should check for duplicate alias/ids?
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78 sheet_contents_dict[row_id] = row_dict
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79 content_dict[sheet_name] = sheet_contents_dict
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80 yaml.dump(content_dict, sys.stdout)
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81 print('YAML -------------')
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82
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83
0
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84 parser = argparse.ArgumentParser()
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85 parser.add_argument('--form', dest='xlsx_path', required=True)
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
86 parser.add_argument('--out_dir', dest='out_path', required=True)
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
87 parser.add_argument('--action', dest='action', required=True)
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
88 parser.add_argument('--vir', dest='viral_submission', required=False, action='store_true')
1
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
diff changeset
89 parser.add_argument('--verbose', dest='verbose', required=False, action='store_true')
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
90 args = parser.parse_args()
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
91
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
92 xl_workbook = xlrd.open_workbook(args.xlsx_path)
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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93
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
94 # PARSE STUDIES
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
95 #################
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
96 xl_sheet = xl_workbook.sheet_by_name('ENA_study')
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
97 if xl_sheet.nrows < 3:
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
98 raise ValueError('No entries found in studies sheet')
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
99 studies_dict = {}
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
100 studies_col = ['alias', 'title', 'study_type', 'study_abstract']
2
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iuc
parents: 1
diff changeset
101 studies_dict, _ = extract_data(xl_sheet, studies_col)
0
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102
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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103 # PARSE SAMPLES
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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104 #################
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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105 xl_sheet = xl_workbook.sheet_by_name('ENA_sample')
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
106 if xl_sheet.nrows < 3:
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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107 raise ValueError('No entries found in samples')
2
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iuc
parents: 1
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108
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
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109 samples_cols_excel = ['alias', 'title', 'scientific_name', 'sample_description']
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
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110 # optional_samples_cols_mapping = {}
0
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iuc
parents:
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111 if args.viral_submission:
2
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parents: 1
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112 # load columns names from the table
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
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113 samples_cols_excel = samples_cols_excel + ['geographic location (country and/or sea)',
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
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114 'host common name', 'host health state',
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
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115 'host sex', 'host scientific name', 'collector name',
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
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116 'collecting institution', 'isolate']
0
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117
2
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parents: 1
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118 samples_dict, samples_optional_cols_loaded = extract_data(xl_sheet, samples_cols_excel,
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
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119 optional_samples_cols_mapping.keys())
0
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iuc
parents:
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120 # PARSE EXPERIMENTS
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iuc
parents:
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121 #################
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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122 xl_sheet = xl_workbook.sheet_by_name('ENA_experiment')
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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123 if xl_sheet.nrows < 3:
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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124 raise ValueError('No experiments found in experiments sheet')
1
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iuc
parents: 0
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125 exp_columns = ['alias', 'title', 'study_alias', 'sample_alias', 'design_description',
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
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126 'library_name', 'library_strategy', 'library_source', 'library_selection',
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
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127 'library_layout', 'insert_size', 'library_construction_protocol',
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents: 0
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128 'platform', 'instrument_model']
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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129
2
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parents: 1
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130 experiments_dict, _ = extract_data(xl_sheet, exp_columns)
0
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131
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iuc
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132 # PARSE RUNS SHEET
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iuc
parents:
diff changeset
133 #################
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
134 xl_sheet = xl_workbook.sheet_by_name('ENA_run')
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
135 if xl_sheet.nrows < 3:
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
136 raise ValueError('No entries found in runs sheet')
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
137 run_cols = ['alias', 'experiment_alias', 'file_name', 'file_format']
2
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
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diff changeset
138 runs_dict, _ = extract_data(xl_sheet, run_cols)
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
139
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iuc
parents:
diff changeset
140 # WRITE HEADERS TO TABLES
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
141 studies_table = open(pathlib.Path(args.out_path) / 'studies.tsv', 'w')
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
142 studies_table.write('\t'.join(['alias', 'status', 'accession', 'title', 'study_type',
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
143 'study_abstract', 'pubmed_id', 'submission_date']) + '\n')
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
144 samples_table = open(pathlib.Path(args.out_path) / 'samples.tsv', 'w')
2
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
145
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
146 samples_cols = ['alias', 'title', 'scientific_name', 'sample_description']
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
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diff changeset
147 # extend the samples_cols list to add the ones that are filled by the CLI
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
148 samples_cols = samples_cols + ['status', 'accession', 'taxon_id', 'submission_date']
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
149 if args.viral_submission:
2
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iuc
parents: 1
diff changeset
150 # extend the samples columns with the viral specific data
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iuc
parents: 1
diff changeset
151 samples_cols = samples_cols + ['geographic_location', 'host_common_name',
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
152 'host_subject_id', 'host_health_state', 'host_sex',
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
153 'host_scientific_name', 'collector_name',
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
154 'collecting_institution', 'isolate']
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
155 if len(samples_optional_cols_loaded) > 0:
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
156 for optional_cols_excel in samples_optional_cols_loaded:
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
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diff changeset
157 samples_cols.append(optional_samples_cols_mapping[optional_cols_excel])
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents: 1
diff changeset
158 samples_table.write('\t'.join(samples_cols) + '\n')
0
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
159
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iuc
parents:
diff changeset
160 experiments_table = open(pathlib.Path(args.out_path) / 'experiments.tsv', 'w')
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
161 experiments_table.write('\t'.join(['alias', 'status', 'accession', 'title', 'study_alias',
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
162 'sample_alias', 'design_description', 'library_name',
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
163 'library_strategy', 'library_source', 'library_selection',
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
164 'library_layout', 'insert_size', 'library_construction_protocol',
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
165 'platform', 'instrument_model', 'submission_date']) + '\n')
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
166
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iuc
parents:
diff changeset
167 runs_table = open(pathlib.Path(args.out_path) / 'runs.tsv', 'w')
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff changeset
168 runs_table.write('\t'.join(['alias', 'status', 'accession', 'experiment_alias', 'file_name',
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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169 'file_format', 'file_checksum', 'submission_date']) + '\n')
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170 action = args.action
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171
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172 # WRITE DICTIONARIES TO TABLE FILES
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173
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174 # ADD A TIMESTAMP TO THE ALIAS? SEEMS LIKE ENA REQUIRES ALL ENTRIES FOR A WEBIN TO HAVE UNIQUE IDS?
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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175 # dt_oobj = datetime.now(tz=None)
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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176 # timestamp = dt_oobj.strftime("%Y%m%d_%H:%M:%S")
1
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177 runs_included = []
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178 exp_included = []
0
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179 for study_alias, study in studies_dict.items():
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180 # study_alias = study_alias + '_' + timestamp
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181 studies_table.write('\t'.join([study_alias, action, 'ENA_accession', study['title'],
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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182 study['study_type'], study['study_abstract'], '',
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iuc
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183 'ENA_submission_data']) + '\n') # assuming no pubmed_id
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184 for sample_alias, sample in samples_dict.items():
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185 # sample_alias = sample_alias + '_' + timestamp
2
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186 samples_row_values = [sample_alias, sample['title'], sample['scientific_name'],
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187 sample['sample_description'], action, 'ena_accession',
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188 'tax_id_updated_by_ENA', 'ENA_submission_date']
0
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189 if args.viral_submission:
2
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190 # add the values that are unique for the viral samples
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191 if sample['collector name'] == '':
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192 sample['collector name'] = 'unknown'
2
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193 samples_row_values = samples_row_values + \
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194 [sample['geographic location (country and/or sea)'], sample['host common name'],
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195 'host subject id', sample['host health state'], sample['host sex'],
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196 sample['host scientific name'], sample['collector name'],
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197 sample['collecting institution'], sample['isolate']]
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198 # add the (possible) optional columns values
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199 if len(samples_optional_cols_loaded) > 0:
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200 for optional_col in samples_optional_cols_loaded:
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201 # parse values stored as in excel date format (=float)
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202 if optional_col in ('collection date', 'receipt date'):
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203 # check if excel stored it as date
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
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204 if isinstance(sample[optional_col], float):
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
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205 year, month, day, hour, minute, second = xlrd.xldate_as_tuple(
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
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206 sample[optional_col], xl_workbook.datemode)
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207 month = "{:02d}".format(month)
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208 day = "{:02d}".format(day)
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209 hour = "{:02d}".format(hour)
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210 minute = "{:02d}".format(minute)
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
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211 second = "{:02d}".format(second)
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212 # format it as 2008-01-23T19:23:10
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213 sample[optional_col] = str(year) + '-' + str(month) + '-' + str(day) + \
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
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214 'T' + str(hour) + ':' + str(minute) + ':' + str(second)
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
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215 # excel stores everything as float so I need to check if
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
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216 # the value was actually an int and keep it as int
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217 if isinstance(sample[optional_col], float):
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218 if int(sample[optional_col]) == sample[optional_col]:
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219 # it is not really a float but an int
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220 sample[optional_col] = int(sample[optional_col])
9e2df763086c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
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221 samples_row_values.append(str(sample[optional_col]))
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222 samples_table.write('\t'.join(samples_row_values) + '\n')
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223
0
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224 for exp_alias, exp in experiments_dict.items():
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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225 # should I check here if any experiment has a study or sample alias that is incorrect?
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226 # (not listed in the samples or study dict)
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227 # process the experiments for this sample
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228 if exp['sample_alias'] == sample_alias:
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229 lib_alias = 'library_' + exp_alias + '_' + exp['sample_alias']
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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230 experiments_table.write('\t'.join([exp_alias, action, 'accession_ena', exp['title'],
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231 exp['study_alias'], sample_alias,
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232 exp['design_description'], lib_alias,
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233 exp['library_strategy'], exp['library_source'],
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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234 exp['library_selection'],
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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235 exp['library_layout'].lower(),
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236 str(int(exp['insert_size'])),
382518f24d6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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237 exp['library_construction_protocol'],
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238 exp['platform'], exp['instrument_model'],
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iuc
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239 'submission_date_ENA']) + '\n')
1
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240 exp_included.append(exp_alias)
0
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241 for run_alias, run in runs_dict.items():
1
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242 # check that the experiments library_layout is set to paired
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243 # when multiple entries are associated with the same run alias
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244 if not isinstance(run, list):
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245 runs_list = [run]
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246 else:
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247 runs_list = run
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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248 for run_entry in runs_list:
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iuc
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249 if run_entry['experiment_alias'] == exp_alias:
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iuc
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250 runs_table.write('\t'.join([run_alias, action, 'ena_run_accession',
57251c760cab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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251 exp_alias, run_entry['file_name'],
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252 FILE_FORMAT, 'file_checksum',
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iuc
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253 'submission_date_ENA']) + '\n')
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254 runs_included.append(run_alias)
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255
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256 # check if any experiment or run was not associated with any sample
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257 for run in runs_dict.keys():
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258 if run not in runs_included:
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259 print(f'The run {run} is listed in the runs section but not associated with any \
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260 used experiment')
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261
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262 for exp in experiments_dict.keys():
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263 if exp not in exp_included:
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264 print(f'The experiment {exp} is listed in the experiments section but not associated \
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265 with any used sample')
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266
0
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267 studies_table.close()
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268 samples_table.close()
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269 experiments_table.close()
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270 runs_table.close()
1
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271
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272 if args.verbose:
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273 paste_xls2yaml(args.xlsx_path)