def get_args():
global fi
global prop
global misc
global properties_file
global genome_name
fi = fileutils()
# Assign description to the help doc
parser = argparse.ArgumentParser(
description='Script downloading genome files')
parser.add_argument('-p',
'--properties_file',
type=str,
help='''Please provide the properties file,
which including workdir''',
required=True)
parser.add_argument('-g',
'--genome_name',
type=str,
help='''Please provide the genome name
which is provided by genome_list.txt''',
required=True)
args = parser.parse_args()
# check args
fi.check_exist(args.properties_file)
properties_file = args.properties_file
prop = properties(properties_file)
misc = misc()
misc.check_genome_avl(prop.get_attrib("available_genomes"),
args.genome_name)
# define variables
genome_name = args.genome_name
print("properties_file:", properties_file)
print("genome_name:", genome_name)
FI.copy_file_add_prefix(tg_out_file, outdir, prefix + "_")
for fastqc_out_file in fastqc_out_files:
FI.copy_file_to_destdir(fastqc_out_file, qcdir)
FI.copy_file_to_destdir(fastqc_out_file.replace(".zip", ".html"),
qcdir)
command("cp -p {}.html {}".format(multiqc_out_prefix, qcdir)).run_comm(0)
if if_dedup:
for deduped_fq in deduped_fqs:
FI.copy_file_add_prefix(deduped_fq, outdir, prefix + "_")
if __name__ == '__main__':
global FI
global MISC
FI = fileutils()
MISC = misc()
get_args()
print("\n", "Properties attributes:\n", prop.__dict__)
#run the initiation code
initiate()
#execute the main part of the program
execute()
#post execution code
post_process()
print(os.path.realpath(__file__) + " DONE")
def execute():
print "executing..."
global identifier
identifier = "ID"
generate_cluster3()
create_image_input_file()
generate_images()
def post_process():
print "post_processing..."
fi.copy_file_to_destdir(workdir + "/" + out_image_fname, outdir)
if __name__ == '__main__':
getVar = lambda searchList, ind: [searchList[i] for i in ind]
misc = misc()
get_args()
print "\n", "Properties attributes:"
print prop.__dict__
#run_blast the initiation code
initiate()
#execute the main part of the program
execute()
#post execution code
post_process()
