diff process_xlsx.py @ 0:382518f24d6d draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/process_xlsx.py	Sat Nov 28 09:45:44 2020 +0000
@@ -0,0 +1,173 @@
+import argparse
+import pathlib
+import sys
+
+import xlrd
+
+
+FILE_FORMAT = 'fastq'
+
+
+def extract_data(xl_sheet, expected_columns):
+    """
+    1. Check that the columns I expect are present in the sheet
+    (any order and mixed with others, it's just a verification that
+    the user filled the correct template)
+    2. Fill a dictionary with the rows data indexed by first column in list"""
+    sheet_columns = {}
+    for sh_col in range(xl_sheet.ncols):
+        if xl_sheet.cell(0, sh_col).value in expected_columns:
+            if xl_sheet.cell(0, sh_col).value in sheet_columns.keys():
+                sys.exit("Duplicated columns")
+            else:
+                sheet_columns[xl_sheet.cell(0, sh_col).value] = sh_col
+    for col in range(len(expected_columns)):
+        assert expected_columns[col] in sheet_columns.keys(), \
+            "Expected column %s not found" % expected_columns[col]
+
+    # fetch rows in a dict
+    data_dict = {}
+    # the first of the expected columns will be the index
+    index_col = sheet_columns[expected_columns[0]]
+    # skip first 2 rows: column names + comments rows
+    for row_id in range(2, xl_sheet.nrows):
+        row_dict = {}
+        for col in range(1, len(expected_columns)):
+            sheet_col_index = sheet_columns[expected_columns[col]]
+            row_dict[expected_columns[col]] = xl_sheet.cell(row_id, sheet_col_index).value
+        # should check for duplicate alias/ids?
+        data_dict[xl_sheet.cell(row_id, index_col).value] = row_dict
+    return data_dict
+
+
+parser = argparse.ArgumentParser()
+parser.add_argument('--form', dest='xlsx_path', required=True)
+parser.add_argument('--out_dir', dest='out_path', required=True)
+parser.add_argument('--action', dest='action', required=True)
+parser.add_argument('--vir', dest='viral_submission', required=False, action='store_true')
+args = parser.parse_args()
+
+xl_workbook = xlrd.open_workbook(args.xlsx_path)
+
+# PARSE STUDIES
+#################
+xl_sheet = xl_workbook.sheet_by_name('ENA_study')
+if xl_sheet.nrows < 3:
+    raise ValueError('No entries found in studies sheet')
+studies_dict = {}
+studies_col = ['alias', 'title', 'study_type', 'study_abstract']
+studies_dict = extract_data(xl_sheet, studies_col)
+
+# PARSE SAMPLES
+#################
+xl_sheet = xl_workbook.sheet_by_name('ENA_sample')
+if xl_sheet.nrows < 3:
+    raise ValueError('No entries found in samples')
+if args.viral_submission:
+    samples_cols = ['alias', 'title', 'scientific_name', 'sample_description',
+                    'geographic location (country and/or sea)', 'host common name',
+                    'host health state', 'host sex', 'host scientific name', 'collector name',
+                    'collection date', 'collecting institution', 'isolate']
+else:
+    samples_cols = ['alias', 'title', 'scientific_name', 'sample_description']
+samples_dict = extract_data(xl_sheet, samples_cols)
+
+# PARSE EXPERIMENTS
+#################
+xl_sheet = xl_workbook.sheet_by_name('ENA_experiment')
+if xl_sheet.nrows < 3:
+    raise ValueError('No experiments found in experiments sheet')
+exp_columns = ['alias', 'title', 'study_alias', 'sample_alias', 'design_description', 'library_name',
+               'library_strategy', 'library_source', 'library_selection', 'library_layout',
+               'insert_size', 'library_construction_protocol', 'platform', 'instrument_model']
+experiments_dict = extract_data(xl_sheet, exp_columns)
+
+# PARSE RUNS SHEET
+#################
+xl_sheet = xl_workbook.sheet_by_name('ENA_run')
+if xl_sheet.nrows < 3:
+    raise ValueError('No entries found in runs sheet')
+run_cols = ['alias', 'experiment_alias', 'file_name', 'file_format']
+runs_dict = extract_data(xl_sheet, run_cols)
+
+# WRITE HEADERS TO TABLES
+studies_table = open(pathlib.Path(args.out_path) / 'studies.tsv', 'w')
+studies_table.write('\t'.join(['alias', 'status', 'accession', 'title', 'study_type',
+                               'study_abstract', 'pubmed_id', 'submission_date']) + '\n')
+samples_table = open(pathlib.Path(args.out_path) / 'samples.tsv', 'w')
+if args.viral_submission:
+    samples_table.write('\t'.join(['alias', 'status', 'accession', 'title', 'scientific_name',
+                                   'taxon_id', 'sample_description', 'collection_date',
+                                   'geographic_location', 'host_common_name', 'host_subject_id',
+                                   'host_health_state', 'host_sex', 'host_scientific_name',
+                                   'collector_name', 'collecting_institution', 'isolate',
+                                   'submission_date']) + '\n')
+else:
+    samples_table.write('\t'.join(['alias', 'status', 'accession', 'title', 'scientific_name',
+                                   'taxon_id', 'sample_description', 'submission_date']) + '\n')
+
+experiments_table = open(pathlib.Path(args.out_path) / 'experiments.tsv', 'w')
+experiments_table.write('\t'.join(['alias', 'status', 'accession', 'title', 'study_alias',
+                                   'sample_alias', 'design_description', 'library_name',
+                                   'library_strategy', 'library_source', 'library_selection',
+                                   'library_layout', 'insert_size', 'library_construction_protocol',
+                                   'platform', 'instrument_model', 'submission_date']) + '\n')
+
+runs_table = open(pathlib.Path(args.out_path) / 'runs.tsv', 'w')
+runs_table.write('\t'.join(['alias', 'status', 'accession', 'experiment_alias', 'file_name',
+                            'file_format', 'file_checksum', 'submission_date']) + '\n')
+action = args.action
+
+# WRITE  DICTIONARIES TO TABLE FILES
+
+# ADD A TIMESTAMP TO THE ALIAS? SEEMS LIKE ENA REQUIRES ALL ENTRIES FOR A WEBIN TO HAVE UNIQUE IDS?
+# dt_oobj = datetime.now(tz=None)
+# timestamp = dt_oobj.strftime("%Y%m%d_%H:%M:%S")
+for study_alias, study in studies_dict.items():
+    # study_alias = study_alias + '_' + timestamp
+    studies_table.write('\t'.join([study_alias, action, 'ENA_accession', study['title'],
+                                   study['study_type'], study['study_abstract'], '',
+                                   'ENA_submission_data']) + '\n')  # assuming no pubmed_id
+for sample_alias, sample in samples_dict.items():
+    # sample_alias = sample_alias + '_' + timestamp
+    if args.viral_submission:
+        if sample['collector name'] == '':
+            sample['collector name'] = 'unknown'
+        samples_table.write('\t'.join([sample_alias, action, 'ena_accession', sample['title'],
+                                       sample['scientific_name'], 'tax_id_updated_by_ENA',
+                                       sample['sample_description'], sample['collection date'],
+                                       sample['geographic location (country and/or sea)'],
+                                       sample['host common name'], 'host subject id',
+                                       sample['host health state'], sample['host sex'],
+                                       sample['host scientific name'], sample['collector name'],
+                                       sample['collecting institution'], sample['isolate'],
+                                       'ENA_submission_date']) + '\n')
+    else:
+        samples_table.write('\t'.join([sample_alias, action, 'ena_accession', sample['title'],
+                                       sample['scientific_name'], 'tax_id_updated_by_ENA',
+                                       sample['sample_description']]) + '\n')
+    for exp_alias, exp in experiments_dict.items():
+        # should I check here if any experiment has a study or sample alias that is incorrect?
+        # (not listed in the samples or study dict)
+        # process the experiments for this sample
+        if exp['sample_alias'] == sample_alias:
+            lib_alias = 'library_' + exp_alias + '_' + exp['sample_alias']
+            experiments_table.write('\t'.join([exp_alias, action, 'accession_ena', exp['title'],
+                                               exp['study_alias'], sample_alias,
+                                               exp['design_description'], lib_alias,
+                                               exp['library_strategy'], exp['library_source'],
+                                               exp['library_selection'],
+                                               exp['library_layout'].lower(),
+                                               str(int(exp['insert_size'])),
+                                               exp['library_construction_protocol'],
+                                               exp['platform'], exp['instrument_model'],
+                                               'submission_date_ENA']) + '\n')
+            for run_alias, run in runs_dict.items():
+                if run['experiment_alias'] == exp_alias:
+                    runs_table.write('\t'.join([run_alias, action, 'ena_run_accession', exp_alias,
+                                                run['file_name'], FILE_FORMAT, 'file_checksum',
+                                                'submission_date_ENA']) + '\n')
+studies_table.close()
+samples_table.close()
+experiments_table.close()
+runs_table.close()