Mercurial > repos > simonl > agile_wrapper
view 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
author | simonl |
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date | Tue, 07 Jun 2011 16:22:51 -0400 |
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#!/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__()