comparison extract_tables.py @ 1:57251c760cab draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"

0:382518f24d6d

import argparse
import json
import pathlib
from datetime import datetime

FILE_FORMAT = 'fastq'

parser = argparse.ArgumentParser()
parser.add_argument('--studies', dest='studies_json_path', required=True)

                                               exp['library_construction_protocol'],
                                               exp['platform'], exp['instrument_model'],
                                               'submission_date_ENA']) + '\n')
            run_index = 0
            # exp['runs'] is a list of lists
            for run in exp['runs']:
                run_index += 1
                run_alias = '.'.join(['run_' + str(run_index), str(exp_index), str(sample_index)]) \
                            + '_' + timestamp
                for file_entry in run:
                    runs_table.write('\t'.join([run_alias, action, 'ena_run_accession', exp_alias,
                                                file_entry, FILE_FORMAT, 'file_checksum',
                                                'submission_date_ENA']) + '\n')

studies_table.close()

1:57251c760cab

import argparse
import json
import pathlib
from datetime import datetime

"""
Parse the configfile generated by the Galaxy tool.
This file is JSON-formatted and should be converted to a set of tabular files.
"""

FILE_FORMAT = 'fastq'

parser = argparse.ArgumentParser()
parser.add_argument('--studies', dest='studies_json_path', required=True)

                                               exp['library_construction_protocol'],
                                               exp['platform'], exp['instrument_model'],
                                               'submission_date_ENA']) + '\n')
            run_index = 0
            # exp['runs'] is a list of lists
            for (base_run, run_files) in exp['runs']:
                run_index += 1
                if base_run != '':
                    run_alias = base_run
                else:
                    # no alias provided, generated a unique one
                    run_alias = '_'.join(['run_' + str(run_index), str(exp_index),
                                          str(sample_index)]) + '_' + timestamp
                for file_entry in run_files:
                    runs_table.write('\t'.join([run_alias, action, 'ena_run_accession', exp_alias,
                                                file_entry, FILE_FORMAT, 'file_checksum',
                                                'submission_date_ENA']) + '\n')

studies_table.close()