# Read configuration files config = util.readConfigurationFiles() header = config.getboolean("server", "PBS_header") ppn = config.get("cellrangercount", "ppn") mem = config.get("cellrangercount", "mem") vmem = config.get("cellrangercount", "vmem") genome = config.get("project", "genome") cellrangerTranscriptome = config.get(genome, "cellrangerTranscriptome") localcores = config.get("cellrangercount", "localcores") localmem = config.get("cellrangercount", "localmem") # Read samples file. samplesDataFrame = util.readSamplesFile() # Create scripts directory, if it does not exist yet, and cd to it. if not os.path.exists(scriptsDirectory): os.mkdir(scriptsDirectory) os.chdir(scriptsDirectory) # Cycle through all the samples and write the cellrangercount scripts. for index, row in samplesDataFrame.iterrows(): sample = row["sample"] # Create script file. scriptName = "cellrangercount_" + sample + ".sh" script = open(scriptName, 'w') if header: util.writeHeader(script, config, "cellrangercount") script.write("cellranger count " + "\\\n")
outputDirectory = os.path.abspath(args.outputDirectory) # Read configuration files config = util.readConfigurationFiles() header = config.getboolean("server", "PBS_header") trim = config.getboolean("project", "trim") stranded = config.getboolean("project", "stranded") genome = config.get("project", "genome") genomeFile = config.get(genome, "genomeFile") gtfFile = config.get(genome, "gtfFile") processors = config.get("stringtie", "processors") # Read samples file. samplesFile = util.readSamplesFile() # Create scripts directory, if it does not exist yet, and cd to it. if not os.path.exists(scriptsDirectory): os.mkdir(scriptsDirectory) os.chdir(scriptsDirectory) # Create output directory, if it does not exist yet. if not os.path.exists(outputDirectory): os.makedirs(outputDirectory) ######################## # stringtie.sh scripts # ######################## for index, row in samplesFile.iterrows(): sample = row["sample"]
header = config.getboolean("server", "PBS_header") stranded = config.getboolean("project", "stranded") if genome is "Configuration file value": if config.has_option("project", "genome"): genome = config.get("project", "genome") else: sys.exit("No reference genome was specified at the command line or in the configuration file.") genomeFile = config.get(genome, "genomeFile") gtfFile = config.get(genome, "gtfFile") bowtieIndex = config.get(genome, "bowtie1Index") processors = config.get("bowtie1", 'processors') k = config.get("bowtie1", "k") v = config.get("bowtie1", "v") # Read samples file. samplesFile = util.readSamplesFile(inputDirectory) # Create scripts directory, if it does not exist yet, and cd to it. if not os.path.exists(scriptsDirectory): os.mkdir(scriptsDirectory) os.chdir(scriptsDirectory) # Create output directories, if they do not exist yet.. if not os.path.exists(outputDirectory): os.makedirs(outputDirectory) # Cycle through all the samples and write the bowtie scripts. for index, row in samplesFile.iterrows(): sample = row["sample"] # Create output directories if not os.path.exists(outputDirectory + "/" + sample):