diff data_manager/data_manager_fetch_motifs.py @ 0:ba049ce65693 draft

Initial upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_fetch_motifs.py	Sun Jan 11 19:21:52 2015 -0500
@@ -0,0 +1,73 @@
+#!/usr/bin/env python
+#Dan Blankenberg
+
+import sys
+import os
+import tempfile
+import shutil
+import optparse
+import urllib2
+#import uuid
+from ftplib import FTP
+import tarfile
+import zipfile
+import gzip
+import bz2
+
+from galaxy.util.json import from_json_string, to_json_string
+
+CHUNK_SIZE = 2**20 #1mb
+
+def download_motif_databases( data_manager_dict, params, target_directory, motif_db ):
+    TEST_DOWNLOAD_URL = 'http://gehlenborg.com/wp-content/uploads/motif/pouya_test_motifs.bed.bgz'
+    #TO DO: Add tbi file
+
+    url = TEST_DOWNLOAD_URL
+    fasta_reader = urllib2.urlopen( url )
+    
+    data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, params )
+    _add_data_table_entry( data_manager_dict, data_table_entry )
+
+def _add_data_table_entry( data_manager_dict, data_table_entry ):
+    data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
+    data_manager_dict['data_tables']['all_fasta'] = data_manager_dict['data_tables'].get( 'all_fasta', [] )
+    data_manager_dict['data_tables']['all_fasta'].append( data_table_entry )
+    return data_manager_dict
+
+def _stream_fasta_to_file( fasta_stream, target_directory, params, close_stream=True ):
+    fasta_base_filename = "pouya_test_motifs.bed.bgz"
+    fasta_filename = os.path.join( target_directory, fasta_base_filename )
+    fasta_writer = open( fasta_filename, 'wb+' )
+    
+    while True:
+        buffer = fasta_stream.read(CHUNK_SIZE)
+        if not buffer:
+            break
+
+        fasta_writer.write(buffer)
+
+    fasta_stream.close()
+    fasta_writer.close()
+    
+    return dict( value="test", name="Test Pouya Subset (hg19)", path=fasta_base_filename )
+
+def main():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option( '-m', '--motif_db', dest='motif_db', action='store', type="string", default=None, help='motif_db' )
+    (options, args) = parser.parse_args()
+    
+    filename = args[0]
+    
+    params = from_json_string( open( filename ).read() )
+    target_directory = params[ 'output_data' ][0]['extra_files_path']
+    os.mkdir( target_directory )
+    data_manager_dict = {}
+    
+    #Fetch the Motif Database
+    download_motif_databases( data_manager_dict, params, target_directory, motif_db )
+    
+    #save info to json file
+    open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
+        
+if __name__ == "__main__": main()