--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/megablast_wrapper.py	Mon May 19 12:33:49 2014 -0400
@@ -0,0 +1,127 @@
+#!/usr/bin/env python
+"""
+run megablast for metagenomics data
+
+usage: %prog [options]
+   -d, --db_build=d: The database to use
+   -i, --input=i: Input FASTQ candidate file
+   -w, --word_size=w: Size of best perfect match
+   -c, --identity_cutoff=c: Report hits at or above this identity
+   -e, --eval_cutoff=e: Expectation value cutoff
+   -f, --filter_query=f: Filter out low complexity regions
+   -x, --index_dir=x: Data index directory
+   -o, --output=o: Output file
+   
+usage: %prog db_build input_file word_size identity_cutoff eval_cutoff filter_query index_dir output_file
+"""
+
+# This version (April 26, 2012) replaces megablast with blast+ blastn
+# There is now no need to augment NCBI-formatted databases and these can be
+# directly downloaded from NCBI ftp site
+
+import os, subprocess, sys, tempfile
+from bx.cookbook import doc_optparse
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def stop_err( msg ):
+    sys.stderr.write( "%s\n" % msg )
+    sys.exit()
+
+def __main__():
+    #Parse Command Line
+    options, args = doc_optparse.parse( __doc__ )
+    query_filename = options.input.strip() # -query
+    output_filename = options.output.strip() # -out
+    mega_word_size = options.word_size        # -word_size
+    mega_iden_cutoff = options.identity_cutoff      # -perc_identity
+    mega_evalue_cutoff = options.eval_cutoff      # -evalue
+    mega_temp_output = tempfile.NamedTemporaryFile().name
+    GALAXY_DATA_INDEX_DIR = options.index_dir
+    DB_LOC = "%s/blastdb.loc" % GALAXY_DATA_INDEX_DIR
+
+    # megablast parameters
+    try:
+        int( mega_word_size )    
+    except:
+        stop_err( 'Invalid value for word size' )
+    try:
+        float( mega_iden_cutoff )
+    except:
+        stop_err( 'Invalid value for identity cut-off' )
+    try:
+        float( mega_evalue_cutoff )
+    except:
+        stop_err( 'Invalid value for Expectation value' )
+
+    if not os.path.exists( os.path.split( options.db_build )[0] ):
+        stop_err( 'Cannot locate the target database directory. Please check your location file.' )
+
+    try:
+        threads = int( os.environ['GALAXY_SLOTS'])
+    except Exception:
+        threads = 8
+    # arguments for megablast
+    megablast_command = "blastn -task megablast -db %s -query %s -out %s -outfmt '6 qseqid sgi slen ppos length mismatch gaps qstart qend sstart send evalue bitscore' -num_threads %d -word_size %s -perc_identity %s -evalue %s -dust %s > /dev/null" \
+        % ( options.db_build, query_filename, mega_temp_output, threads, mega_word_size, mega_iden_cutoff, mega_evalue_cutoff, options.filter_query ) 
+
+    print megablast_command
+
+    tmp = tempfile.NamedTemporaryFile().name
+    try:
+        tmp_stderr = open( tmp, 'wb' )
+        proc = subprocess.Popen( args=megablast_command, shell=True, stderr=tmp_stderr.fileno() )
+        returncode = proc.wait()
+        tmp_stderr.close()
+        # get stderr, allowing for case where it's very large
+        tmp_stderr = open( tmp, 'rb' )
+        stderr = ''
+        buffsize = 1048576
+        try:
+            while True:
+                stderr += tmp_stderr.read( buffsize )
+                if not stderr or len( stderr ) % buffsize != 0:
+                    break
+        except OverflowError:
+            pass
+        tmp_stderr.close()
+        if returncode != 0:
+            raise Exception, stderr
+        if os.path.exists( tmp ):
+            os.unlink( tmp )
+    except Exception, e:
+        if os.path.exists( mega_temp_output ):
+            os.unlink( mega_temp_output )
+        if os.path.exists( tmp ):
+            os.unlink( tmp )
+        stop_err( 'Cannot execute megaablast. ' + str( e ) )
+
+    output = open( output_filename, 'w' )
+    invalid_lines = 0
+    for i, line in enumerate( file( mega_temp_output ) ):
+        line = line.rstrip( '\r\n' )
+        fields = line.split()
+        try:
+            # convert the last column (bit-score as this is causing problem in filter tool) to float
+            fields[-1] = float( fields[-1] )
+            new_line = "%s\t%0.1f" % ( '\t'.join( fields[:-1] ), fields[-1] )
+        except:
+            new_line = line
+            invalid_lines += 1
+        output.write( "%s\n" % new_line )
+    output.close()
+
+    if os.path.exists( mega_temp_output ):
+        os.unlink( mega_temp_output ) #remove the tempfile that we just reformatted the contents of
+
+    if invalid_lines:
+        print "Unable to parse %d lines. Keep the default format." % invalid_lines
+
+    # megablast generates a file called error.log, if empty, delete it, if not, show the contents
+    if os.path.exists( './error.log' ):
+        for i, line in enumerate( file( './error.log' ) ):
+            line = line.rstrip( '\r\n' )
+            print line
+        os.remove( './error.log' )
+
+if __name__ == "__main__" : __main__()