def main(): argc = len(sys.argv) argv = sys.argv if argc == 1: print "Usage: bin-seq.py input-sequences bin-results-filename" return # load default settings pre.default_settings() pre.seqs_file = argv[1] pre.bin_file = argv[2] bindistri_file = pre.bin_file + 'distri' if len(pre.seqs_file) == 0: print 'The sequence file is not defined.' return if not os.path.exists(pre.seqs_file): print 'The sequence file %s is not correctly defined.' % pre.seqs_file return print ' Input sequence file:', pre.seqs_file print_section_title('Sequence Binning') print ' Sequence binning model:', pre.binmodel print ' Taxonomy map file:', pre.taxonomy cmd = '%s -m %s -s %s -t %s -b %s -d %s' % \ (pre.bin_seqs, pre.binmodel, pre.seqs_file, pre.taxonomy, pre.bin_file, bindistri_file) call(cmd, shell = True, stdout = PIPE) print ' Binning result file:', pre.bin_file return
def program_prepair(): # define program used in this script programs = pre.default_settings() global svmscale, svmtrain global subset_py, grid_py, is_win32 is_win32 = (sys.platform == 'win32') svmscale = pre.svm_scale svmtrain = pre.svm_train subset_py = pre.subset_py grid_py = pre.grid_py
def main(): argc = len(sys.argv) argv = sys.argv if argc == 1: print "Usage: domain-search.py input-sequences search-results-filename" return # load default settings pre.default_settings() pre.seqs_file = argv[1] pre.hit_file = argv[2] if len(pre.seqs_file) == 0: print 'The sequence file is not defined.' return if not os.path.exists(pre.seqs_file): print 'The sequence file %s is not correctly defined.' % pre.seqs_file return print_section_title('Novel predict') print ' Blast searches against known database:', pre.blast_db alc_file = pre.seqs_file + '.alc' csqa_file = pre.seqs_file + '.csqa' pre.project_name = pre.seqs_file pre.hit_file = argv[2] cmd = '%s -p -n %s -a -s %s' % (pre.get_data, pre.project_name, pre.seqs_file) call(cmd, shell = True, stdout = PIPE) cmd = '%s -n %s -s %s -c %s -q 1' % (pre.get_data, pre.project_name, pre.seqs_file, alc_file) call(cmd, shell = True, stdout = PIPE) cmd = '%s -i %s -d %s -m 8 -v 1 -b 1 -e 1 -o %s' % (pre.rpsblast, csqa_file, pre.blast_db, pre.hit_file) call(cmd, shell = True, stdout = PIPE) rm_files([alc_file, csqa_file]) print ' Blast search results save in:', pre.hit_file return
def main(): argc = len(sys.argv) argv = sys.argv if argc == 1: print parse_command.__doc__ return if command_line_parser(argv, '-h', '--help', False)[0]: print detail_help.__doc__ return # load default settings pre.default_settings() # parse settings from command line parse_command(argv) if len(pre.seqs_file) == 0: print 'The sequence file is not defined.' return if not os.path.exists(pre.seqs_file): print 'The sequence file %s is not correctly defined.' % pre.seqs_file return print_section_title('Start MetaGUN Prediction') print ' Input sequence file:', pre.seqs_file print ' Project name:', pre.project_name print_section_title('Sequence Binning') if pre.exists_bin_file == False: pre.bin_file = pre.project_name + '.bin' bindistri_file = pre.project_name + '.bindistri' print ' Sequence binning model:', pre.binmodel print ' Taxonomy map file:', pre.taxonomy cmd = '%s -m %s -s %s -t %s -b %s -d %s' % \ (pre.bin_seqs, pre.binmodel, pre.seqs_file, pre.taxonomy, pre.bin_file, bindistri_file) call(cmd, shell = True, stdout = PIPE) print ' Binning result file:', pre.bin_file else: print ' Use given binning result:', pre.bin_file uni_pred_file = pre.project_name + '.uni-pred' novel_pred_file = pre.project_name + '.novel-pred' if pre.run_uni_pred: uni_pred(uni_pred_file) if pre.run_novel_pred: novel_pred(novel_pred_file) metagun_file = pre.project_name + '.metagun' if pre.run_uni_pred and pre.run_novel_pred: cmd = '%s -a %s -b %s --a+b -o %s' % (pre.metalocs_operate, novel_pred_file, uni_pred_file, metagun_file) call(cmd, shell=True, stdout=PIPE) rm_files([uni_pred_file, novel_pred_file]) elif pre.run_uni_pred and not pre.run_novel_pred: os.rename(uni_pred_file, metagun_file) elif not pre.run_uni_pred and pre.run_novel_pred: os.rename(novel_pred_file, metagun_file) if not pre.run_metatisa: print_section_title('MetaGUN Prediction Over') print ' Final predictions output', metagun_file return print_section_title('TIS Refinement') metatisa_file = metagun_file + '.metatisa' cmd = '%s -s %s -l %s -b %s -p %s -f MED -o %s -c %s -w %i' % \ (pre.metatisa, pre.seqs_file, metagun_file, pre.bin_file, pre.tismodel, metatisa_file, pre.metatisa_settings, is_win) call(cmd, shell=True, stdout=PIPE) if os.path.exists(metagun_file): os.remove(metagun_file) os.rename(metatisa_file, metagun_file) print_section_title('MetaGUN Prediction Over') print ' Final predictions output', metagun_file return