comparison data_manager/data_manager_snpEff_databases.py @ 13:c3cdca7f40a2 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_snpeff commit 225ce35e1c3514cdba7a3637eba9aee964fa85f7

12:617d95d798fa

#!/usr/bin/env python
import json
import optparse
import os
import subprocess
import sys


def fetch_databases(data_manager_dict, target_directory):
    if not os.path.exists(target_directory):
        os.makedirs(target_directory)

    if return_code:
        sys.exit(return_code)
    data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
    data_manager_dict['data_tables']['snpeffv_databases'] = data_manager_dict['data_tables'].get('snpeffv_databases', [])
    data_table_entries = []
    with open(databases_path, 'r') as fh:
        for line in fh:
            fields = line.split('\t')
            if len(fields) >= 2:
                genome_version = fields[0].strip()

                    continue
                # snpeff test genome
                if genome_version == '30c2c903' or fields[1].strip() == 'TestCase' or fields[1].strip().startswith('Test_'):
                    continue
                description = fields[1].strip() + ' : ' + genome_version
                data_table_entries.append(dict(value=genome_version, name=description))
    data_manager_dict['data_tables']['snpeffv_databases'] = data_table_entries
    return data_manager_dict


def main():

13:c3cdca7f40a2

#!/usr/bin/env python
import json
import optparse
import os
import re
import subprocess
import sys


def getSnpeffVersion():
    snpeff_version = 'SnpEff ?.?'
    args = ['snpEff', '-version']
    try:
        version_output = subprocess.check_output(args, shell=False).decode()
    except subprocess.CalledProcessError as e:
        sys.exit(e.returncode)
    m = re.match(r'^(SnpEff)\s*(\d+\.\d+).*$', version_output)
    if m:
        snpeff_version = m.groups()[0] + m.groups()[1]
    return snpeff_version


def fetch_databases(data_manager_dict, target_directory):
    if not os.path.exists(target_directory):
        os.makedirs(target_directory)

    if return_code:
        sys.exit(return_code)
    data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
    data_manager_dict['data_tables']['snpeffv_databases'] = data_manager_dict['data_tables'].get('snpeffv_databases', [])
    data_table_entries = []
    snpeff_version = getSnpeffVersion()

    with open(databases_path, 'r') as fh:
        for line in fh:
            fields = line.split('\t')
            if len(fields) >= 2:
                genome_version = fields[0].strip()

                    continue
                # snpeff test genome
                if genome_version == '30c2c903' or fields[1].strip() == 'TestCase' or fields[1].strip().startswith('Test_'):
                    continue
                description = fields[1].strip() + ' : ' + genome_version
                data_table_entries.append(dict(key=snpeff_version + '_' + genome_version, version=snpeff_version, value=genome_version, name=description))
    data_manager_dict['data_tables']['snpeffv_databases'] = data_table_entries
    return data_manager_dict


def main():