def main(): rExists = os.system("which r") if rExists == 256: print "\n\nYou need to install r first\n\n" quit() rscriptExists = os.system("which Rscript") if rscriptExists == 256: print "\n\nYou need to install Rscript first\n\n" quit() path2files, treesFolder, chromoSizeFile, mappingFile, majorClade, minorsXmajor, majors, criterion, m_interval = get_parameters( ) # Counting minor clades and filtering by criterion result_counts = TreesCriteria_counts.count(path2files, treesFolder, majorClade, mappingFile, int(criterion)) print "total genes = " + result_counts.split(",")[0] print "total trees = " + result_counts.split(",")[1] # Mapping the information result_mapIntervals = Intervals.mapIntervals(path2files, m_interval, chromoSizeFile) print "number of chromosomes: " + str( result_mapIntervals['number of chromosomes']) print "map size: " + str(result_mapIntervals['map size']) print "genes mapped: " + str(result_mapIntervals['genes mapped']) # Redistributing the loci that are not clearly in an interval. result_mapInfoHelper = MapInfoHelper.redistributeLoci(path2files) print result_mapInfoHelper result_matrix = BuildMapMatrix.BuildMatrix(path2files, minorsXmajor, majors, m_interval) os.system("rm *.pyc")