diff Users/oconnorlab/Desktop/agile/agile_wrapper.py @ 0:d6a426afaa46 default tip

Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Users/oconnorlab/Desktop/agile/agile_wrapper.py	Tue Jun 07 16:22:51 2011 -0400
@@ -0,0 +1,93 @@
+#!/usr/bin/env python
+
+import os, sys, tempfile
+
+assert sys.version_info[:2] >= (2.4)
+
+def stop_err( msg ):
+    sys.stderr.write( "%s\n" % msg )
+    sys.exit()
+    
+def check_nib_file( dbkey, GALAXY_DATA_INDEX_DIR ):
+    nib_file = "%s/alignseq.loc" % GALAXY_DATA_INDEX_DIR
+    nib_path = ''
+    nibs = {}
+    for i, line in enumerate( file( nib_file ) ):
+        line = line.rstrip( '\r\n' )
+        if line and not line.startswith( "#" ):
+            fields = line.split( '\t' )
+            if len( fields ) < 3:
+                continue
+            if fields[0] == 'seq':
+                nibs[( fields[1] )] = fields[2]
+    if nibs.has_key( dbkey ):
+        nib_path = nibs[( dbkey )]
+    return nib_path
+
+def check_twobit_file( dbkey, GALAXY_DATA_INDEX_DIR ):
+    twobit_file = "%s/twobit.loc" % GALAXY_DATA_INDEX_DIR
+    twobit_path = ''
+    twobits = {}
+    for i, line in enumerate( file( twobit_file ) ):
+        line = line.rstrip( '\r\n' )
+        if line and not line.startswith( "#" ): 
+            fields = line.split( '\t' )
+            if len( fields ) < 2:
+                continue
+            twobits[( fields[0] )] = fields[1]
+    if twobits.has_key( dbkey ):
+        twobit_path = twobits[( dbkey )]
+    return twobit_path
+
+def __main__():
+    # I/O
+    source_format = sys.argv[1]        # 0: dbkey; 1: upload file
+    target_file = sys.argv[2]
+    query_file = sys.argv[3]
+    output_file = sys.argv[4]
+    max_sims = sys.argv[5]
+    tile_size = sys.argv[6]
+    max_freq = sys.argv[7]
+    out_type = sys.argv[8]
+    all_match = sys.argv[9]
+    
+    GALAXY_DATA_INDEX_DIR = sys.argv[10]
+
+    all_files = []
+    if source_format == '0':
+        # check target genome
+        dbkey = target_file
+        nib_path = check_nib_file( dbkey, GALAXY_DATA_INDEX_DIR )
+        twobit_path = check_twobit_file( dbkey, GALAXY_DATA_INDEX_DIR )
+        if not os.path.exists( nib_path ) and not os.path.exists( twobit_path ):
+            stop_err("No sequences are available for %s, request them by reporting this error." % dbkey)
+    
+        # check the query file, see whether all of them are legitimate sequence
+        if nib_path and os.path.isdir( nib_path ):
+            compress_files = os.listdir(nib_path)
+            target_path = nib_path
+        elif twobit_path:
+            compress_files = [twobit_path]
+            target_path = ""
+        else:
+            stop_err("Requested genome build has no available sequence.")
+            
+        for file in compress_files:
+            file = "%s/%s" % ( target_path, file )
+            file = os.path.normpath(file)
+            all_files.append(file)
+    else:
+        all_files = [target_file]
+        
+    for detail_file_path in all_files:
+        output_tempfile = tempfile.NamedTemporaryFile().name
+        if all_match == "true":
+	        command = "agile %s %s -maxSIMs=%s -tileSize=%s -maxFreq=%s -out=%s -all %s 2>&1" % ( detail_file_path, query_file, max_sims, tile_size, max_freq, out_type, output_tempfile )
+        else:
+	        command = "agile %s %s -maxSIMs=%s -tileSize=%s -maxFreq=%s -out=%s %s 2>&1" % ( detail_file_path, query_file, max_sims, tile_size, max_freq, out_type, output_tempfile )		
+
+        os.system( command )
+        os.system( 'cat %s >> %s' % ( output_tempfile, output_file ) )
+        os.remove( output_tempfile )
+        
+if __name__ == '__main__': __main__()