def run_rum(self): """Run the fastqc program from the command line. Assumes that it is on your PATH. """ cmd = self.make_command() utils.safe_run(cmd, shell=False)
def run_fastqc(self): """Run the fastqc program from the command line. Assumes that it is on your PATH. """ cmd = self.make_command() utils.safe_run(cmd, shell=False)
def run_collect_rnaseq_metrics(input, output, params=None): """Set up and run the Picard CollectRnaSeqMetrics program. """ # # Let a parser argument handle setting up arguments and options # parser = argparse.ArgumentParser() # # Add Picard arguments # picard = Picard.PicardBase() # parser = picard.argparse(parser) # Update input and output from global config object picard_params = config['picard_params'] picard_params['input'] = input picard_params['output'] = output # Set up using the default arguments, specifying the input and output files since they are required! cmdline = "--jar=%(jar_file)s --input=%(input)s --output=%(output)s --ref_flat=%(ref_flat)s --ref_file=%(ref_file)s CollectRnaSeqMetrics --minimum_length=%(minimum_length)s --chart_output=%(chart_output)s --metric_accumulation_level=%(metric_accumulation_level)s --stop_after=%(stop_after)s" % picard_params # args = parser.parse_args(cmdline.split()) # # Run the function for collecting RNASeq metrics # args.func(args) picard_cmd = "python -m ccrngspy.tasks.Picard %s" % cmdline stdout, stderr = utils.safe_run(picard_cmd, shell=False) logger.debug("stdout = %s, err = %s" % (stdout, stderr))
def run_sort_sam(input, output, params=None): """Set up and run the Picard SortSam program. """ # # Let a parser argument handle setting up arguments and options # parser = argparse.ArgumentParser() # # Add Picard arguments # picard = Picard.PicardBase() # parser = picard.argparse(parser) # Update input and output from global config object picard_params = config['picard_sortsam_params'] picard_params['input'] = input picard_params['output'] = output logger.debug("picard_params = %s" % (picard_params,)) # Set up using the default arguments, specifying the input and output files since they are required! cmdline = "--jar=%(jar_file)s --input=%(input)s --output=%(output)s --sort_order=%(sort_order)s SortSam" % picard_params # args = parser.parse_args(cmdline.split()) # # Run the function for collecting RNASeq metrics # args.func(args) picard_cmd = "python -m ccrngspy.tasks.Picard %s" % cmdline stdout, stderr = utils.safe_run(picard_cmd, shell=False) logger.debug("stdout = %s, err = %s" % (stdout, stderr))
def run_rum(input, output, params=None): """Run RUM on paired reads. """ # Let a parser argument handle setting up arguments and options parser = argparse.ArgumentParser() # Add Picard arguments rum = RUM.RUMrunner() parser = rum.argparse(parser) # Update input and output from global config object rum_params = config['rum_params'] rum_params['input'] = input ## fastq read files rum_params['file1'] = input[0] rum_params['file2'] = input[1] rum_params['sample'] = params['sample'] cmdline = "--rum_config_file=%(config_file)s --rum_run_name=%(sample)s --rum_outdir=%(output_dir)s/%(sample)s --rum_read_files %(file1)s %(file2)s " % rum_params args = parser.parse_args(cmdline.split()) rum.set_options(args) rum_command = rum.make_command() stdout, stderr = utils.safe_run(rum_command, shell=False) logger.debug("stdout = %s, err = %s" % (stdout, stderr))
def run_fastqc(input, output, params=None): """Set up and run the fastqc program. """ # Let a parser argument handle setting up arguments and options parser = argparse.ArgumentParser() # Add Picard arguments fastqc = FastQC.FastQC() parser = fastqc.argparse(parser) # Update input and output from global config object fastqc_params = config['fastqc_params'] fastqc_params['input'] = input cmdline = "--outdir=%(output_dir)s --threads=%(threads)s %(input)s" % fastqc_params args = parser.parse_args(cmdline.split()) fastqc.set_options(args) # fastqc_task = FastQC.FastQC(input_files=[input], output_directory=config['fastqc_params']['output_dir']) fastqc_command = fastqc.make_command() # if fastqc_params['run_type'] == 'remote': # stdout, stderr = utils.safe_qsub_run(fastqc_command, jobname="run_fastqc") # elif fastqc_params['run_type'] == 'local': stdout, stderr = utils.safe_run(fastqc_command, shell=False) logger.debug("stdout = %s, stderr = %s" % (stdout, stderr)) # post task, touch output file! of = file(output, mode="w") of.close()