Mercurial > repos > sanbi-uwc > data_manager_novoalign_index_builder

annotate data_manager/novoalign_index_builder.py @ 1:4d67344bdea7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 1f4717cce284465cddbb221a5ca4d1f601c14f84
author sanbi-uwc
date Thu, 03 Mar 2016 06:28:09 -0500
parents 85fbd52dbb36
children e51fb8188ed9
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
1 #!/usr/bin/env python
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
2 # Z. Mashologu (SANBI-UWC)
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
3 #import dict as dict
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
4 import os
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
5 import shutil
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
6 import optparse
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
7 import urllib2
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
8 import logging
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
9 log = logging.getLogger( __name__ )
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
10
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
11 from json import loads, dumps
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
12
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
13 def cleanup_before_exit( tmp_dir ):
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
14 if tmp_dir and os.path.exists( tmp_dir ):
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
15 shutil.rmtree( tmp_dir )
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
16
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
17 def _stream_fasta_to_file( fasta_stream, target_directory, params, close_stream=True ):
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
18 fasta_base_filename = "%s.fa" % sequence_id
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
19 fasta_filename = os.path.join( target_directory, fasta_base_filename )
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
20 fasta_writer = open( fasta_filename, 'wb+' )
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
21
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
22 if isinstance( fasta_stream, list ) and len( fasta_stream ) == 1:
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
23 fasta_stream = fasta_stream[0]
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
24
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
25 if isinstance( fasta_stream, list ):
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
26 last_char = None
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
27 for fh in fasta_stream:
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
28 if last_char not in [ None, '\n', '\r' ]:
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
29 fasta_writer.write( '\n' )
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
30 while True:
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
31 data = fh.read( CHUNK_SIZE )
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
32 if data:
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
33 fasta_writer.write( data )
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
34 last_char = data[-1]
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
35 else:
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
36 break
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
37 if close_stream:
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
38 fh.close()
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
39 else:
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
40 while True:
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
41 data = fasta_stream.read( CHUNK_SIZE )
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
42 if data:
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
43 fasta_writer.write( data )
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
44 else:
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
45 break
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
46 if close_stream:
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
47 fasta_stream.close()
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
48
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
49 fasta_writer.close()
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
50
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
51 return dict( path=fasta_base_filename )
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
52
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
53 def download_from_url( data_manager_dict, params, target_directory, dbkey, sequence_id, sequence_name ):
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
54 #TODO: we should automatically do decompression here
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
55 urls = filter( bool, map( lambda x: x.strip(), params['param_dict']['reference_source']['user_url'].split( '\n' ) ) )
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
56 fasta_reader = [ urllib2.urlopen( url ) for url in urls ]
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
57
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
58 data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, params )
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
59 _add_data_table_entry( data_manager_dict, data_table_entry )
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
60
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
61 def download_from_history( data_manager_dict, params, target_directory):
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
62 #TODO: allow multiple FASTA input files
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
63 input_filename = params['param_dict']['reference_source']['input_fasta']
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
64 if isinstance( input_filename, list ):
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
65 fasta_reader = [ open( filename, 'rb' ) for filename in input_filename ]
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
66 else:
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
67 fasta_reader = open( input_filename )
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
68
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
69 data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, params )
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
70 _add_data_table_entry( data_manager_dict, data_table_entry )
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
71
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
72 def copy_from_directory( data_manager_dict, params, target_directory ):
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
73 input_filename = params['param_dict']['reference_source']['fasta_filename']
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
74 create_symlink = params['param_dict']['reference_source']['create_symlink'] == 'create_symlink'
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
75 if create_symlink:
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
76 data_table_entry = _create_symlink( input_filename, target_directory )
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
77 else:
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
78 if isinstance( input_filename, list ):
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
79 fasta_reader = [ open( filename, 'rb' ) for filename in input_filename ]
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
80 else:
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
81 fasta_reader = open( input_filename )
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
82 data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, params )
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
83 _add_data_table_entry( data_manager_dict, data_table_entry )
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
84
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
85 def _create_symlink( input_filename, target_directory ):
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
86 fasta_base_filename = "%s.fa" % sequence_id
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
87 fasta_filename = os.path.join( target_directory, fasta_base_filename )
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
88 os.symlink( input_filename, fasta_filename )
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
89 return dict( path=fasta_base_filename )
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
90
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
91 REFERENCE_SOURCE_TO_DOWNLOAD = dict( url=download_from_url, history=download_from_history, directory=copy_from_directory )
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
92
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
93 def main():
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
94 #Parse Command Line
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
95 parser = optparse.OptionParser()
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
96 parser.add_option( '-d', '--data_table_name' )
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
97 (options, args) = parser.parse_args()
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
98
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
99 filename = args[0]
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
100
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
101 params = loads( open( filename ).read() )
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
102 target_directory = params[ 'output_data' ][0]['extra_files_path']
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
103 os.mkdir( target_directory )
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
104 data_manager_dict = {}
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
105
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
106 #Fetch the FASTA
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
107 REFERENCE_SOURCE_TO_DOWNLOAD[ params['param_dict']['reference_source']['reference_source_selector'] ]( data_manager_dict, params, target_directory )
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
108
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
109 #save info to json file
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
110 open( filename, 'wb' ).write( dumps( data_manager_dict ) )
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
111
85fbd52dbb36 planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf
sanbi-uwc
parents:
diff changeset
112 if __name__ == "__main__": main()