Mercurial > repos > bgruening > data_manager_diamond_database_builder

comparison data_manager/data_manager_diamond_database_builder.py @ 0:ce62d0912b10 draft

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Imported from capsule None
author bgruening
date Sun, 08 Feb 2015 10:05:20 -0500
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children 5a0d0bee4f8d
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-1:000000000000 0:ce62d0912b10
1 #!/usr/bin/env python
2 import sys
3 import os
4 import tempfile
5 import shutil
6 import optparse
7 import urllib2
8 import subprocess
9 from ftplib import FTP
10 import tarfile
11 import zipfile
12 import gzip
13 import bz2
14
15 from galaxy.util.json import from_json_string, to_json_string
16
17 CHUNK_SIZE = 2**20 #1mb
18
19 def cleanup_before_exit( tmp_dir ):
20 if tmp_dir and os.path.exists( tmp_dir ):
21 shutil.rmtree( tmp_dir )
22
23
24 def stop_err(msg):
25 sys.stderr.write(msg)
26 sys.exit(1)
27
28
29 def _get_files_in_ftp_path( ftp, path ):
30 path_contents = []
31 ftp.retrlines( 'MLSD %s' % ( path ), path_contents.append )
32 return [ line.split( ';' )[ -1 ].lstrip() for line in path_contents ]
33
34
35 def _get_stream_readers_for_tar( file_obj, tmp_dir ):
36 fasta_tar = tarfile.open( fileobj=file_obj, mode='r:*' )
37 return [ fasta_tar.extractfile( member ) for member in fasta_tar.getmembers() ]
38
39
40 def _get_stream_readers_for_zip( file_obj, tmp_dir ):
41 fasta_zip = zipfile.ZipFile( file_obj, 'r' )
42 rval = []
43 for member in fasta_zip.namelist():
44 fasta_zip.extract( member, tmp_dir )
45 rval.append( open( os.path.join( tmp_dir, member ), 'rb' ) )
46 return rval
47
48
49 def _get_stream_readers_for_gzip( file_obj, tmp_dir ):
50 return [ gzip.GzipFile( fileobj=file_obj, mode='rb' ) ]
51
52
53 def _get_stream_readers_for_bz2( file_obj, tmp_dir ):
54 return [ bz2.BZ2File( file_obj.name, 'rb' ) ]
55
56
57 def download_from_ncbi( data_manager_dict, params, target_directory, database_id, database_name ):
58 NCBI_FTP_SERVER = 'ftp.ncbi.nlm.nih.gov'
59 NCBI_DOWNLOAD_PATH = '/blast/db/FASTA/'
60 COMPRESSED_EXTENSIONS = [ ( '.tar.gz', _get_stream_readers_for_tar ), ( '.tar.bz2', _get_stream_readers_for_tar ), ( '.zip', _get_stream_readers_for_zip ), ( '.gz', _get_stream_readers_for_gzip ), ( '.bz2', _get_stream_readers_for_bz2 ) ]
61
62 ncbi_identifier = params['param_dict']['reference_source']['requested_identifier']
63 ftp = FTP( NCBI_FTP_SERVER )
64 ftp.login()
65
66 path_contents = _get_files_in_ftp_path( ftp, NCBI_DOWNLOAD_PATH )
67
68 ncbi_file_name = None
69 get_stream_reader = None
70 ext = None
71 for ext, get_stream_reader in COMPRESSED_EXTENSIONS:
72 if "%s%s" % ( ncbi_identifier, ext ) in path_contents:
73 ncbi_file_name = "%s%s%s" % ( NCBI_DOWNLOAD_PATH, ncbi_identifier, ext )
74 break
75
76 if not ncbi_file_name:
77 raise Exception( 'Unable to determine filename for NCBI database for %s: %s' % ( ncbi_identifier, path_contents ) )
78
79 tmp_dir = tempfile.mkdtemp( prefix='tmp-data-manager-ncbi-' )
80 ncbi_fasta_filename = os.path.join( tmp_dir, "%s%s" % ( ncbi_identifier, ext ) )
81
82 fasta_base_filename = "%s.fa" % database_id
83 fasta_filename = os.path.join( target_directory, fasta_base_filename )
84 fasta_writer = open( fasta_filename, 'wb+' )
85
86 tmp_extract_dir = os.path.join ( tmp_dir, 'extracted_fasta' )
87 os.mkdir( tmp_extract_dir )
88
89 tmp_fasta = open( ncbi_fasta_filename, 'wb+' )
90
91 ftp.retrbinary( 'RETR %s' % ncbi_file_name, tmp_fasta.write )
92
93 tmp_fasta.flush()
94 tmp_fasta.seek( 0 )
95
96 fasta_readers = get_stream_reader( tmp_fasta, tmp_extract_dir )
97
98 data_table_entry = _stream_fasta_to_file( fasta_readers, target_directory, database_id, database_name, params )
99 _add_data_table_entry( data_manager_dict, data_table_entry )
100
101 for fasta_reader in fasta_readers:
102 fasta_reader.close()
103 tmp_fasta.close()
104 cleanup_before_exit( tmp_dir )
105
106
107 def download_from_url( data_manager_dict, params, target_directory, database_id, database_name ):
108 #TODO: we should automatically do decompression here
109 urls = filter( bool, map( lambda x: x.strip(), params['param_dict']['reference_source']['user_url'].split( '\n' ) ) )
110 fasta_reader = [ urllib2.urlopen( url ) for url in urls ]
111
112 data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, database_id, database_name, params )
113 _add_data_table_entry( data_manager_dict, data_table_entry )
114
115
116 def download_from_history( data_manager_dict, params, target_directory, database_id, database_name ):
117 #TODO: allow multiple FASTA input files
118 input_filename = params['param_dict']['reference_source']['input_fasta']
119 if isinstance( input_filename, list ):
120 fasta_reader = [ open( filename, 'rb' ) for filename in input_filename ]
121 else:
122 fasta_reader = open( input_filename )
123
124 data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, database_id, database_name, params )
125 _add_data_table_entry( data_manager_dict, data_table_entry )
126
127
128 def copy_from_directory( data_manager_dict, params, target_directory, database_id, database_name ):
129 input_filename = params['param_dict']['reference_source']['fasta_filename']
130 create_symlink = params['param_dict']['reference_source']['create_symlink'] == 'create_symlink'
131 if create_symlink:
132 data_table_entry = _create_symlink( input_filename, target_directory, database_id, database_name )
133 else:
134 if isinstance( input_filename, list ):
135 fasta_reader = [ open( filename, 'rb' ) for filename in input_filename ]
136 else:
137 fasta_reader = open( input_filename )
138 data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, database_id, database_name, params )
139 _add_data_table_entry( data_manager_dict, data_table_entry )
140
141
142 def _add_data_table_entry( data_manager_dict, data_table_entry ):
143 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
144 data_manager_dict['data_tables']['diamond_database'] = data_manager_dict['data_tables'].get( 'diamond_database', [] )
145 data_manager_dict['data_tables']['diamond_database'].append( data_table_entry )
146 return data_manager_dict
147
148
149 def _stream_fasta_to_file( fasta_stream, target_directory, database_id, database_name, params, close_stream=True ):
150 fasta_base_filename = "%s.fa" % database_id
151 fasta_filename = os.path.join( target_directory, fasta_base_filename )
152
153 temp_fasta = tempfile.NamedTemporaryFile( delete=False, suffix=".fasta" )
154 temp_fasta.close()
155 fasta_writer = open( temp_fasta.name, 'wb+' )
156
157 if isinstance( fasta_stream, list ) and len( fasta_stream ) == 1:
158 fasta_stream = fasta_stream[0]
159
160 if isinstance( fasta_stream, list ):
161 last_char = None
162 for fh in fasta_stream:
163 if last_char not in [ None, '\n', '\r' ]:
164 fasta_writer.write( '\n' )
165 while True:
166 data = fh.read( CHUNK_SIZE )
167 if data:
168 fasta_writer.write( data )
169 last_char = data[-1]
170 else:
171 break
172 if close_stream:
173 fh.close()
174 else:
175 while True:
176 data = fasta_stream.read( CHUNK_SIZE )
177 if data:
178 fasta_writer.write( data )
179 else:
180 break
181 if close_stream:
182 fasta_stream.close()
183
184 fasta_writer.close()
185
186 args = [ 'diamond', 'makedb', '--in', temp_fasta.name, '--db', fasta_filename]
187
188 tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-diamond-database-builder-stderr" )
189 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() )
190 return_code = proc.wait()
191 if return_code:
192 tmp_stderr.flush()
193 tmp_stderr.seek(0)
194 print >> sys.stderr, "Error building diamond database:"
195 while True:
196 chunk = tmp_stderr.read( CHUNK_SIZE )
197 if not chunk:
198 break
199 sys.stderr.write( chunk )
200 sys.exit( return_code )
201 tmp_stderr.close()
202 os.remove( temp_fasta.name )
203 return dict( value=database_id, name=database_name, db_path="%s.dmnd" % fasta_base_filename )
204
205
206 def _create_symlink( input_filename, target_directory, database_id, database_name ):
207 fasta_base_filename = "%s.fa" % database_id
208 fasta_filename = os.path.join( target_directory, fasta_base_filename )
209 os.symlink( input_filename, fasta_filename )
210 return dict( value=database_id, name=database_name, db_path=fasta_base_filename )
211
212
213 REFERENCE_SOURCE_TO_DOWNLOAD = dict( ncbi=download_from_ncbi, url=download_from_url, history=download_from_history, directory=copy_from_directory )
214
215 def main():
216 #Parse Command Line
217 parser = optparse.OptionParser()
218 parser.add_option( '-d', '--dbkey_description', dest='dbkey_description', action='store', type="string", default=None, help='dbkey_description' )
219 (options, args) = parser.parse_args()
220
221 filename = args[0]
222
223 params = from_json_string( open( filename ).read() )
224 target_directory = params[ 'output_data' ][0]['extra_files_path']
225 os.mkdir( target_directory )
226 data_manager_dict = {}
227
228 database_id = params['param_dict']['database_id']
229 database_name = params['param_dict']['database_name']
230
231 #Fetch the FASTA
232 REFERENCE_SOURCE_TO_DOWNLOAD[ params['param_dict']['reference_source']['reference_source_selector'] ]( data_manager_dict, params, target_directory, database_id, database_name )
233
234 #save info to json file
235 open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
236
237 if __name__ == "__main__":
238 main()