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()
