def main():
"""Runs SSC.
For command line help, run with the '-h' flag.
"""
args = get_args()
dataset, chrom, tool = common.process_args(args, tool_name=TOOL)
if not dataset or not tool:
return
tool_path = tool.get_dir_path()
out_path = tool.get_out_dir(dataset.name)
spacer = os.path.join(tool_path, SPACER_PATH)
spacer_out = os.path.join(out_path, "%s_spacer.txt" % chrom.name)
tool.run_bash(["-i", chrom.get_path(), "-o", spacer_out], spacer)
ssc = tool.get_bin_path()
matrix = os.path.join(tool_path, MATRIX_PATH)
ssc_out = os.path.join(out_path, RAW_OUT_NAME % chrom.name)
stdout, stderr = tool.run_bash(
["-i", spacer_out, "-o", ssc_out, "-m", matrix, "-l", "30"], ssc)
if stderr: print stderr
if stdout: print stdout
tools_common.create_csv(chrom, tool, RAW_OUT_NAME)
tools_common.normalise(chrom, tool)
def main():
"""Runs sgRNA Scorer 2.0.
For command line help, run with the '-h' flag.
"""
args = get_args()
dataset, chrom, tool = common.process_args(args, tool_name=TOOL)
if not dataset or not tool:
return
tool.chdir()
script_path = os.path.join(tool.get_dir_path(), tool.bin_path)
params = [
"-d", args.dataset,
"-c", str(args.chr),
"-o", RAW_OUT_NAME % chrom.name,
"-p", "3", "-s", "20", "-l", "NGG",
]
process = subprocess.Popen(
["python", script_path] + params,
stdout=subprocess.PIPE, stderr=subprocess.PIPE)
outs, errs = process.communicate()
print(outs)
print(errs)
tools_common.create_csv(chrom, tool, RAW_OUT_NAME)
tools_common.normalise(chrom, tool)
def main():
"""Runs phytoCRISP-Ex.
For command line help, run with the '-h' flag.
"""
args = get_args()
dataset, chrom, tool = common.process_args(args, tool_name=TOOL)
if not dataset or not tool:
return
params = ["-g", args.dataset, "-c", chrom.name, "NGG", "G"]
tool.run_bash(params)
shutil.move(
os.path.join(dataset.get_data_path(), SRC_OUT_NAME % chrom.name),
os.path.join(tool.get_out_dir(dataset.name),
DST_OUT_NAME % chrom.name))
tools_common.normalise(chrom, tool)
def main():
"""Runs mm10db.
For command line help, run with the '-h' flag.
"""
args = get_args()
dataset, chrom, tool = common.process_args(args, tool_name=TOOL)
if not dataset or not tool:
return
tool.chdir()
script_params = ["-g", args.dataset, "-c", chrom.name]
out_path = tool.get_out_dir(dataset.name)
# Runs the mm10db pipeline.
for script in SCRIPTS:
tool.run_python(script_params, script)
tools_common.create_csv(chrom, tool, RAW_OUT_NAME)
add_rejected(chrom, out_path)
tools_common.normalise(chrom, tool)
def main():
"""Runs CHOPCHOP.
For command line help, run with the '-h' flag.
"""
args = get_args()
dataset, chrom, tool = common.process_args(args, tool_name=TOOL)
if not dataset or not tool:
return
tool.chdir()
chr_name = chrom.get_name()
out_path = tool.get_out_dir(dataset.name)
config_path = os.path.join(tool.get_dir_path(), CONFIG_FILE)
# Configures and runs CHOPCHOP, and then reverts the configuration file.
config(dataset.get_data_path(), config_path)
params = [
"-G",
dataset.name,
"-o",
os.path.join(out_path, chr_name),
"-F",
"--targets",
chrom.get_path(),
"--chr",
chr_name,
"--scoringMethod",
"ALL",
]
output, _ = tool.run_python(params)
unconfig(config_path)
# Writes the output.
with open(os.path.join(out_path, RAW_OUT_NAME % chr_name), 'w') as txt:
txt.write(output)
tools_common.create_csv(chrom, tool, RAW_OUT_NAME)
tools_common.normalise(chrom, tool)
def main():
"""Runs FlashFry.
For command line help, run with the '-h' flag.
"""
args = get_args()
dataset, chrom, tool = common.process_args(args, tool_name=TOOL)
if not dataset or not tool:
return
chr_path = chrom.get_path()
out_path = tool.get_out_dir(dataset.name)
bin_path = tool.get_bin_path()
chr_name = chrom.get_name()
index_path = os.path.join(out_path, INDEX_NAME % chr_name)
discover_path = os.path.join(out_path, DISCOVER_NAME % chr_name)
targets_path = os.path.join(out_path, RAW_OUT_NAME % chr_name)
cmd_index = [
"java",
"-Xmx4g",
"-jar",
bin_path,
"index",
"--tmpLocation",
out_path,
"--database",
index_path,
"--reference",
chr_path,
"--enzyme",
"spcas9ngg",
]
cmd_discover = [
"java",
"-Xmx4g",
"-jar",
bin_path,
"discover",
"--database",
index_path,
"--fasta",
chr_path,
"--output",
discover_path,
]
cmd_score = [
"java",
"-Xmx4g",
"-jar",
bin_path,
"score",
"--input",
discover_path,
"--output",
targets_path,
"--scoringMetrics",
"doench2014ontarget,moreno2015",
"--database",
index_path,
]
tool.chdir()
_ = subprocess.Popen(cmd_index).wait()
_ = subprocess.Popen(cmd_discover).wait()
_ = subprocess.Popen(cmd_score).wait()
tools_common.create_csv(chrom, tool, RAW_OUT_NAME)
tools_common.normalise(chrom, tool)