Mercurial > repos > iuc > data_manager_bowtie_index_builder
comparison data_manager/bowtie_index_builder.py @ 4:86e9af693a33 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 67d76bc24ec6a5eb145f05416dc2098999897bae
author | iuc |
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date | Fri, 09 Jun 2017 06:12:02 -0400 |
parents | ea5faedd0795 |
children | 08a3583826fa |
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3:ea5faedd0795 | 4:86e9af693a33 |
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1 #!/usr/bin/env python | 1 #!/usr/bin/env python |
2 from __future__ import print_function | |
3 | |
2 import json | 4 import json |
3 import optparse | 5 import optparse |
4 import os | 6 import os |
5 import subprocess | 7 import subprocess |
6 import sys | 8 import sys |
40 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() ) | 42 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() ) |
41 return_code = proc.wait() | 43 return_code = proc.wait() |
42 if return_code: | 44 if return_code: |
43 tmp_stderr.flush() | 45 tmp_stderr.flush() |
44 tmp_stderr.seek(0) | 46 tmp_stderr.seek(0) |
45 print >> sys.stderr, "Error building index:" | 47 print("Error building index:", file=sys.stderr) |
46 while True: | 48 while True: |
47 chunk = tmp_stderr.read( CHUNK_SIZE ) | 49 chunk = tmp_stderr.read( CHUNK_SIZE ) |
48 if not chunk: | 50 if not chunk: |
49 break | 51 break |
50 sys.stderr.write( chunk ) | 52 sys.stderr.write( chunk ) |
60 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry ) | 62 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry ) |
61 return data_manager_dict | 63 return data_manager_dict |
62 | 64 |
63 | 65 |
64 def main(): | 66 def main(): |
65 # Parse Command Line | |
66 parser = optparse.OptionParser() | 67 parser = optparse.OptionParser() |
67 parser.add_option( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' ) | 68 parser.add_option( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' ) |
68 parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' ) | 69 parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' ) |
69 parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' ) | 70 parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' ) |
70 parser.add_option( '-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name' ) | 71 parser.add_option( '-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name' ) |