def runPyCombat(fl): """ This method was added specifically for AltAnalyze version 2.0.8 (not in the original GitHub code) """ print "Running Combat...", expr_input_dir = fl.ExpFile() pheno_dir = formatPhenoFile(fl) moved_exp_dir = export.findParentDir(expr_input_dir) + "Non-Combat/" + export.findFilename(expr_input_dir) try: export.copyFile(expr_input_dir, moved_exp_dir) print "Moved original expression file to:" print "\t" + moved_exp_dir ### now overwrite the origin excluding the commented rows export.cleanFile(expr_input_dir, removeExtra="#") ### remove comments from the original file except Exception: None pheno = pa.read_table(pheno_dir, index_col=0) dat = pa.read_table(expr_input_dir, index_col=0) mod = patsy.dmatrix("group", pheno, return_type="dataframe") t = time.time() # print dat, pheno.batch, mod;sys.exit() ebat = combat(dat, pheno.batch, mod, 0) print "...Combat completed in %.2f seconds" % (time.time() - t) print "Original expression file over-written with batch effect removal results..." ebat.to_csv(expr_input_dir, sep="\t")
def normalizeDataset(filename, output=None, normalization='quantile', platform="3'array"): """ Perform Quantile Normalization on an input expression dataset """ if output == None: output = filename moved_exp_dir = export.findParentDir( filename) + 'Non-Normalized/' + export.findFilename(filename) try: export.copyFile(filename, moved_exp_dir) print 'Moved original expression file to:' print '\t' + moved_exp_dir except Exception: None if normalization == 'Quantile' or normalization == 'quantile': print "Importing data..." sample_expression_db = importExpressionValues(filename) print "Performing quantile normalization..." sample_expression_db = RNASeq.quantileNormalizationSimple( sample_expression_db) exportExpressionData(output, sample_expression_db) elif normalization == 'group': performGroupNormalization(moved_exp_dir, filename, platform) print 'Exported expression input file to:', output
def runPyCombat(fl): """ This method was added specifically for AltAnalyze version 2.0.8 (not in the original GitHub code) """ print 'Running Combat...', expr_input_dir = fl.ExpFile() pheno_dir = formatPhenoFile(fl) moved_exp_dir = export.findParentDir( expr_input_dir) + 'Non-Combat/' + export.findFilename(expr_input_dir) try: export.copyFile(expr_input_dir, moved_exp_dir) print 'Moved original expression file to:' print '\t' + moved_exp_dir ### now overwrite the origin excluding the commented rows export.cleanFile( expr_input_dir, removeExtra='#') ### remove comments from the original file except Exception: None pheno = pa.read_table(pheno_dir, index_col=0) dat = pa.read_table(expr_input_dir, index_col=0) mod = patsy.dmatrix("group", pheno, return_type="dataframe") t = time.time() #print dat, pheno.batch, mod;sys.exit() ebat = combat(dat, pheno.batch, mod, 0) print "...Combat completed in %.2f seconds" % (time.time() - t) print 'Original expression file over-written with batch effect removal results...' ebat.to_csv(expr_input_dir, sep="\t")
def copyReformattedSpeciesMiRAnnotations(type): existing_species_dirs = unique.read_directory('/AltDatabase/ensembl') for species in existing_species_dirs: try: ir = filepath('AltDatabase/ensembl/'+species+'/'+species+'_microRNA-Ensembl-GOElite_'+type+'.txt') er = filepath('GOElite/'+species+'_microRNA-Ensembl-GOElite_'+type+'.txt') export.copyFile(ir, er) print 'Copied miRNA-target database for:',species, type except Exception: null=[] ### Occurs for non-species directories
def transferGOSlimGeneAssociations(selected_species): if selected_species != None: ### Restrict to selected species only current_species_dirs=selected_species else: current_species_dirs = unique.read_directory('/'+database_dir) for species_code in current_species_dirs: try: ens_go_file_dir = filepath(database_dir+'/'+species_code+'/gene-go/Ensembl-GOSlim.txt') goslim_ens_file = filepath(database_dir+'/'+species_code+'/uid-gene/Ensembl-goslim_goa.txt') export.copyFile(goslim_ens_file,ens_go_file_dir) translateToEntrezGene(species_code,ens_go_file_dir) except Exception: null=[]
def copyJunctionFiles(directory): root_dir = getFolders(directory) #print root_dir for top_level in root_dir: ### e.g., try: files = getFiles(directory+'/'+top_level) for file in files: if 'junctions.bed' in file and 'junctionBEDfiles' not in top_level: source_file = directory+'/'+top_level+'/'+file source_file = filepath(source_file) destination_file = directory+'/'+'junctionBEDfiles/'+top_level+'__junctions.bed' destination_file = filepath(destination_file) export.copyFile(source_file,destination_file) print 'copying to:',destination_file except Exception: print 'failed to copy', source_file
def normalizeDataset(filename, output=None): """ Perform Quantile Normalization on an input expression dataset """ print "Importing data..." sample_expression_db = importExpressionValues(filename) print "Performing quantile normalization..." sample_expression_db = RNASeq.quantileNormalizationSimple(sample_expression_db) if output == None: output = filename moved_exp_dir = export.findParentDir(filename) + "Non-Quantile/" + export.findFilename(filename) try: export.copyFile(filename, moved_exp_dir) print "Moved original expression file to:" print "\t" + moved_exp_dir except Exception: None exportExpressionData(output, sample_expression_db) print "Exported expression input file to:", output
def normalizeDataset(filename,output = None, normalization='quantile',platform="3'array"): """ Perform Quantile Normalization on an input expression dataset """ if output==None: output = filename moved_exp_dir = export.findParentDir(filename)+'Non-Normalized/'+export.findFilename(filename) try: export.copyFile(filename, moved_exp_dir) print 'Moved original expression file to:' print '\t'+moved_exp_dir except Exception: None if normalization == 'Quantile' or normalization == 'quantile': print "Importing data..." sample_expression_db = importExpressionValues(filename) print "Performing quantile normalization..." sample_expression_db = RNASeq.quantileNormalizationSimple(sample_expression_db) exportExpressionData(output,sample_expression_db) elif normalization == 'group': performGroupNormalization(moved_exp_dir,filename,platform) print 'Exported expression input file to:',output
def normalizeDataset(filename, output=None): """ Perform Quantile Normalization on an input expression dataset """ print "Importing data..." sample_expression_db = importExpressionValues(filename) print "Performing quantile normalization..." sample_expression_db = RNASeq.quantileNormalizationSimple( sample_expression_db) if output == None: output = filename moved_exp_dir = export.findParentDir( filename) + 'Non-Quantile/' + export.findFilename(filename) try: export.copyFile(filename, moved_exp_dir) print 'Moved original expression file to:' print '\t' + moved_exp_dir except Exception: None exportExpressionData(output, sample_expression_db) print 'Exported expression input file to:', output
def importDomainGeneAssociations(species_code,source_path): try: destination_path = filepath(database_dir+'/'+species_code+'/gene-mapp/Ensembl-Domains.txt') export.copyFile(source_path,destination_path) translateToEntrezGene(species_code,destination_path) except Exception: null=[]