Mercurial > repos > iuc > data_manager_bowtie_index_builder

comparison data_manager/bowtie_index_builder.py @ 4:86e9af693a33 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 67d76bc24ec6a5eb145f05416dc2098999897bae
author iuc
date Fri, 09 Jun 2017 06:12:02 -0400
parents ea5faedd0795
children 08a3583826fa
comparison
equal deleted inserted replaced
3:ea5faedd0795 4:86e9af693a33
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' )