Mercurial > repos > devteam > data_manager_twobit_builder

comparison data_manager/twobit_builder.py @ 2:c9896bb1f03c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 8652f36a3a3838dca989426961561e81432acf4f
author iuc
date Tue, 04 Apr 2017 17:54:54 -0400
parents 26e3ae5f74ed
children ced9f4a48806
comparison
equal deleted inserted replaced
1:298d15849a14 2:c9896bb1f03c
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 #Dan Blankenberg 2 # Dan Blankenberg
3 from __future__ import print_function
3 4
4 import sys, os, tempfile, optparse, uuid, subprocess 5 import optparse
6 import os
7 import subprocess
8 import sys
9 import tempfile
10 from json import dumps, loads
5 11
6 from json import loads, dumps 12 CHUNK_SIZE = 2**20 # 1mb
7 13
8 14
9 CHUNK_SIZE = 2**20 #1mb
10
11 def get_id_name( params, dbkey, fasta_description=None): 15 def get_id_name( params, dbkey, fasta_description=None):
12 #TODO: ensure sequence_id is unique and does not already appear in location file 16 # TODO: ensure sequence_id is unique and does not already appear in location file
13 sequence_id = params['param_dict']['sequence_id'] 17 sequence_id = params['param_dict']['sequence_id']
14 if not sequence_id: 18 if not sequence_id:
15 sequence_id = dbkey #uuid.uuid4() generate and use an uuid 19 sequence_id = dbkey # uuid.uuid4() generate and use an uuid
16 20
17 sequence_name = params['param_dict']['sequence_name'] 21 sequence_name = params['param_dict']['sequence_name']
18 if not sequence_name: 22 if not sequence_name:
19 sequence_name = fasta_description 23 sequence_name = fasta_description
20 if not sequence_name: 24 if not sequence_name:
21 sequence_name = dbkey 25 sequence_name = dbkey
22 return sequence_id, sequence_name 26 return sequence_id, sequence_name
23 27
28
24 def build_twobit( data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name ): 29 def build_twobit( data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name ):
25 twobit_base_name = "%s.2bit" % ( sequence_id ) 30 twobit_base_name = "%s.2bit" % ( sequence_id )
26 twobit_filename = os.path.join( target_directory, twobit_base_name ) 31 twobit_filename = os.path.join( target_directory, twobit_base_name )
27 32
28 args = [ 'faToTwoBit', fasta_filename, twobit_filename ] 33 args = [ 'faToTwoBit', fasta_filename, twobit_filename ]
29 tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-twobit-builder-stderr" ) 34 tmp_stderr = tempfile.NamedTemporaryFile( prefix="tmp-data-manager-twobit-builder-stderr" )
30 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() ) 35 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() )
31 return_code = proc.wait() 36 return_code = proc.wait()
32 if return_code: 37 if return_code:
33 tmp_stderr.flush() 38 tmp_stderr.flush()
34 tmp_stderr.seek(0) 39 tmp_stderr.seek(0)
35 print >> sys.stderr, "Error building index:" 40 print("Error building index:", file=sys.stderr)
36 while True: 41 while True:
37 chunk = tmp_stderr.read( CHUNK_SIZE ) 42 chunk = tmp_stderr.read( CHUNK_SIZE )
38 if not chunk: 43 if not chunk:
39 break 44 break
40 sys.stderr.write( chunk ) 45 sys.stderr.write( chunk )
41 sys.exit( return_code ) 46 sys.exit( return_code )
42 tmp_stderr.close() 47 tmp_stderr.close()
43 #lastz_seqs 48 # lastz_seqs
44 data_table_entry = dict( value=sequence_id, name=sequence_name, path=twobit_base_name ) 49 data_table_entry = dict( value=sequence_id, name=sequence_name, path=twobit_base_name )
45 50
46 _add_data_table_entry( data_manager_dict, "lastz_seqs", data_table_entry ) 51 _add_data_table_entry( data_manager_dict, "lastz_seqs", data_table_entry )
47 #twobit.loc 52 # twobit.loc
48 data_table_entry = dict( value=sequence_id, path=twobit_base_name ) 53 data_table_entry = dict( value=sequence_id, path=twobit_base_name )
49 54
50 _add_data_table_entry( data_manager_dict, "twobit", data_table_entry ) 55 _add_data_table_entry( data_manager_dict, "twobit", data_table_entry )
51 #alignseq 56 # alignseq
52 data_table_entry = dict( type="seq", value=sequence_id, path=twobit_base_name ) 57 data_table_entry = dict( type="seq", value=sequence_id, path=twobit_base_name )
53 58
54 _add_data_table_entry( data_manager_dict, "alignseq_seq", data_table_entry ) 59 _add_data_table_entry( data_manager_dict, "alignseq_seq", data_table_entry )
60
55 61
56 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ): 62 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
57 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) 63 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
58 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] ) 64 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
59 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry ) 65 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
60 return data_manager_dict 66 return data_manager_dict
61 67
68
62 def main(): 69 def main():
63 #Parse Command Line
64 parser = optparse.OptionParser() 70 parser = optparse.OptionParser()
65 parser.add_option( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' ) 71 parser.add_option( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' )
66 parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' ) 72 parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' )
67 parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' ) 73 parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' )
68 (options, args) = parser.parse_args() 74 (options, args) = parser.parse_args()
69 75
70 filename = args[0] 76 filename = args[0]
71 77
72 params = loads( open( filename ).read() ) 78 params = loads( open( filename ).read() )
73 79
74 target_directory = params[ 'output_data' ][0]['extra_files_path'] 80 target_directory = params[ 'output_data' ][0]['extra_files_path']
75 os.mkdir( target_directory ) 81 os.mkdir( target_directory )
76 data_manager_dict = {} 82 data_manager_dict = {}
77 83
78 dbkey = options.fasta_dbkey 84 dbkey = options.fasta_dbkey
79 85
80 if dbkey in [ None, '', '?' ]: 86 if dbkey in [ None, '', '?' ]:
81 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) ) 87 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) )
82 88
83 sequence_id, sequence_name = get_id_name( params, dbkey=dbkey, fasta_description=options.fasta_description ) 89 sequence_id, sequence_name = get_id_name( params, dbkey=dbkey, fasta_description=options.fasta_description )
84 90
85 #build the index 91 # build the index
86 build_twobit( data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name ) 92 build_twobit( data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name )
87 93
88 #save info to json file 94 # save info to json file
89 open( filename, 'wb' ).write( dumps( data_manager_dict ) ) 95 open( filename, 'wb' ).write( dumps( data_manager_dict ) )
90
91 if __name__ == "__main__": main()
92 96
97
98 if __name__ == "__main__":
99 main()