diff data_manager/novoalign_index_builder.py @ 0:85fbd52dbb36 draft

planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit d51fdc6291de173e829a839e98c6c3ae367d84bf

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/novoalign_index_builder.py	Thu Mar 03 05:59:41 2016 -0500
@@ -0,0 +1,112 @@
+#!/usr/bin/env python
+# Z. Mashologu (SANBI-UWC)
+#import dict as dict
+import os
+import shutil
+import optparse
+import urllib2
+import logging
+log = logging.getLogger( __name__ )
+
+from json import loads, dumps
+
+def cleanup_before_exit( tmp_dir ):
+    if tmp_dir and os.path.exists( tmp_dir ):
+        shutil.rmtree( tmp_dir )
+
+def _stream_fasta_to_file( fasta_stream, target_directory, params, close_stream=True ):
+    fasta_base_filename = "%s.fa" % sequence_id
+    fasta_filename = os.path.join( target_directory, fasta_base_filename )
+    fasta_writer = open( fasta_filename, 'wb+' )
+
+    if isinstance( fasta_stream, list ) and len( fasta_stream ) == 1:
+        fasta_stream = fasta_stream[0]
+
+    if isinstance( fasta_stream, list ):
+        last_char = None
+        for fh in fasta_stream:
+            if last_char not in [ None, '\n', '\r' ]:
+                fasta_writer.write( '\n' )
+            while True:
+                data = fh.read( CHUNK_SIZE )
+                if data:
+                    fasta_writer.write( data )
+                    last_char = data[-1]
+                else:
+                    break
+            if close_stream:
+                fh.close()
+    else:
+        while True:
+            data = fasta_stream.read( CHUNK_SIZE )
+            if data:
+                fasta_writer.write( data )
+            else:
+                break
+        if close_stream:
+            fasta_stream.close()
+
+    fasta_writer.close()
+
+    return dict( path=fasta_base_filename )
+
+def download_from_url( data_manager_dict, params, target_directory, dbkey, sequence_id, sequence_name ):
+    #TODO: we should automatically do decompression here
+    urls = filter( bool, map( lambda x: x.strip(), params['param_dict']['reference_source']['user_url'].split( '\n' ) ) )
+    fasta_reader = [ urllib2.urlopen( url ) for url in urls ]
+
+    data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, params )
+    _add_data_table_entry( data_manager_dict, data_table_entry )
+
+def download_from_history( data_manager_dict, params, target_directory):
+    #TODO: allow multiple FASTA input files
+    input_filename = params['param_dict']['reference_source']['input_fasta']
+    if isinstance( input_filename, list ):
+        fasta_reader = [ open( filename, 'rb' ) for filename in input_filename ]
+    else:
+        fasta_reader = open( input_filename )
+
+    data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, params )
+    _add_data_table_entry( data_manager_dict, data_table_entry )
+
+def copy_from_directory( data_manager_dict, params, target_directory ):
+    input_filename = params['param_dict']['reference_source']['fasta_filename']
+    create_symlink = params['param_dict']['reference_source']['create_symlink'] == 'create_symlink'
+    if create_symlink:
+        data_table_entry = _create_symlink( input_filename, target_directory )
+    else:
+        if isinstance( input_filename, list ):
+            fasta_reader = [ open( filename, 'rb' ) for filename in input_filename ]
+        else:
+            fasta_reader = open( input_filename )
+        data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, params )
+    _add_data_table_entry( data_manager_dict, data_table_entry )
+
+def _create_symlink( input_filename, target_directory ):
+    fasta_base_filename = "%s.fa" % sequence_id
+    fasta_filename = os.path.join( target_directory, fasta_base_filename )
+    os.symlink( input_filename, fasta_filename )
+    return dict( path=fasta_base_filename )
+
+REFERENCE_SOURCE_TO_DOWNLOAD = dict( url=download_from_url, history=download_from_history, directory=copy_from_directory )
+
+def main():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option( '-d', '--data_table_name' )
+    (options, args) = parser.parse_args()
+
+    filename = args[0]
+
+    params = loads( open( filename ).read() )
+    target_directory = params[ 'output_data' ][0]['extra_files_path']
+    os.mkdir( target_directory )
+    data_manager_dict = {}
+
+    #Fetch the FASTA
+    REFERENCE_SOURCE_TO_DOWNLOAD[ params['param_dict']['reference_source']['reference_source_selector'] ]( data_manager_dict, params, target_directory )
+
+    #save info to json file
+    open( filename, 'wb' ).write( dumps( data_manager_dict ) )
+
+if __name__ == "__main__": main()
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