Mercurial > repos > rnateam > data_manager_sortmerna_database_downloader
comparison data_manager/data_manager_sortmerna_download.py @ 2:7d2252852f96 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sortmerna_database_downloader commit 4241c1d4b05a177bd2c74f5a139f51d4f65e0b55
author | rnateam |
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date | Tue, 13 Jun 2017 12:03:08 -0400 |
parents | 30bb49887172 |
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1:30bb49887172 | 2:7d2252852f96 |
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2 # Data manager for reference data for the SortMeRNA Galaxy tools | 2 # Data manager for reference data for the SortMeRNA Galaxy tools |
3 | 3 |
4 import argparse | 4 import argparse |
5 import json | 5 import json |
6 import os | 6 import os |
7 import shutil | |
7 import tarfile | 8 import tarfile |
8 import requests | 9 import requests |
9 import subprocess | 10 import subprocess |
10 | 11 |
11 | 12 |
124 file_dir = os.path.join(archive_content_path, "rRNA_databases") | 125 file_dir = os.path.join(archive_content_path, "rRNA_databases") |
125 for filename in os.listdir(file_dir): | 126 for filename in os.listdir(file_dir): |
126 if not filename.endswith("fasta"): | 127 if not filename.endswith("fasta"): |
127 continue | 128 continue |
128 input_filepath = os.path.join(file_dir, filename) | 129 input_filepath = os.path.join(file_dir, filename) |
129 output_filepath = os.path.join(target_dir, filename) | 130 # Extract the db name |
130 # Move file | 131 db_name = os.path.splitext(filename)[0] |
131 os.rename(input_filepath, output_filepath) | 132 # Create the directory where to put the fasta files and indexed files |
133 filedir = os.path.join(target_dir, db_name) | |
134 os.mkdir(filedir) | |
135 fasta_filepath = os.path.join(filedir, "%s.fasta" % db_name) | |
136 indexed_filepath = os.path.join(filedir, db_name) | |
137 # Move the fasta file | |
138 shutil.move(input_filepath, fasta_filepath) | |
132 # Index the file with indexdb_rna | 139 # Index the file with indexdb_rna |
133 command = "indexdb_rna --ref %s,%s" % ( | 140 command = "indexdb_rna --ref %s,%s" % ( |
134 output_filepath, | 141 fasta_filepath, |
135 os.path.splitext(output_filepath)[0]) | 142 indexed_filepath) |
136 process = subprocess.call(command, shell=True ) | 143 process = subprocess.call(command, shell=True ) |
137 # Add entry in the data table | 144 # Add entry in the data table |
138 db_name = os.path.splitext(filename)[0] | |
139 add_data_table_entry( | 145 add_data_table_entry( |
140 data_tables, | 146 data_tables, |
141 "rRNA_databases", | 147 "rRNA_databases", |
142 dict( | 148 dict( |
143 value=version, | 149 value="%s-%s" %(version, db_name), |
144 name=db_name, | 150 name=db_name, |
145 path=output_filepath)) | 151 path=filedir)) |
146 | 152 |
147 | 153 |
148 def download_db(data_tables, version, target_dir): | 154 def download_db(data_tables, version, target_dir): |
149 """Download SortMeRNA database | 155 """Download SortMeRNA database |
150 | 156 |