1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/0a0b01a980ea/ changeset: 0a0b01a980ea user: anton date: 2012-04-26 16:49:38 summary: Fixed number of threads affected #: 1 file
diff -r 0b5cb60e48104bd1df937bd6c7051abfda7190ff -r 0a0b01a980eac2f4c98d317bbde3ff572aca13e9 tools/metag_tools/megablast_wrapper.py --- a/tools/metag_tools/megablast_wrapper.py +++ b/tools/metag_tools/megablast_wrapper.py @@ -15,6 +15,10 @@ 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 galaxy import eggs import pkg_resources; pkg_resources.require( "bx-python" ) @@ -29,11 +33,11 @@ def __main__(): #Parse Command Line options, args = doc_optparse.parse( __doc__ ) - query_filename = options.input.strip() - output_filename = options.output.strip() - mega_word_size = options.word_size # -W - mega_iden_cutoff = options.identity_cutoff # -p - mega_evalue_cutoff = options.eval_cutoff # -e + 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 @@ -56,7 +60,7 @@ stop_err( 'Cannot locate the target database directory. Please check your location file.' )
# 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 2 -word_size %s -perc_identity %s -evalue %s -dust %s > /dev/null" \ + 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 8 -word_size %s -perc_identity %s -evalue %s -dust %s > /dev/null" \ % ( options.db_build, query_filename, mega_temp_output, mega_word_size, mega_iden_cutoff, mega_evalue_cutoff, options.filter_query )
print megablast_command @@ -88,7 +92,7 @@ os.unlink( mega_temp_output ) if os.path.exists( tmp ): os.unlink( tmp ) - stop_err( 'Error indexing reference sequence. ' + str( e ) ) + stop_err( 'Cannot execute megaablast. ' + str( e ) )
output = open( output_filename, 'w' ) invalid_lines = 0 @@ -96,7 +100,7 @@ line = line.rstrip( '\r\n' ) fields = line.split() try: - # convert the last column (causing problem in filter tool) to float + # 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:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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