def run(database: Database, file: str, params, input_format, output_format):
database.download(params["database_bucket"], "crux", "/tmp/crux")
subprocess.call("chmod 755 /tmp/crux", shell=True)
output_dir = "/tmp/percolator-crux-output-{0:f}-{1:d}".format(
input_format["timestamp"], input_format["nonce"])
arguments = [
"--subset-max-train",
str(params["max_train"]),
"--quick-validation",
"T",
"--output-dir",
output_dir,
]
command = "cd /tmp; ./crux percolator {0:s} {1:s}".format(
file, " ".join(arguments))
try:
subprocess.check_output(command, stderr=subprocess.STDOUT, shell=True)
except subprocess.CalledProcessError as exc:
print("Status : FAIL", exc.returncode, exc.output)
raise exc
output_files = []
for item in ["target.{0:s}".format(params["output"])]:
input_file = "{0:s}/percolator.{1:s}.txt".format(output_dir, item)
output_format["ext"] = "percolator"
output_file = "/tmp/{0:s}".format(util.file_name(output_format))
os.rename(input_file, output_file)
output_files.append(output_file)
shutil.rmtree(output_dir)
return output_files
def run(database: Database, file: str, params, input_format, output_format):
database.download(params["database_bucket"], "crux", "/tmp/crux")
subprocess.call("chmod 755 /tmp/crux", shell=True)
output_dir = "/tmp/confidence-crux-output-{0:f}-{1:d}".format(input_format["timestamp"], input_format["nonce"])
arguments = [
"--output-dir", output_dir,
]
command = "cd /tmp; ./crux assign-confidence {0:s} {1:s}".format(file, " ".join(arguments))
subprocess.check_output(command, shell=True)
output_files = []
input_file = "{0:s}/assign-confidence.target.txt".format(output_dir)
output_format["ext"] = "confidence"
output_file = "/tmp/{0:s}".format(util.file_name(output_format))
os.rename(input_file, output_file)
output_files.append(output_file)
return output_files
def run(database: Database, file: str, params, input_format, output_format):
if "species" in params:
species = params["species"]
else:
raise Exception("Tide needs species parameter specified")
database.download(params["database_bucket"], "{0:s}/fasta".format(species),
"/tmp/fasta")
database.download(params["database_bucket"], "crux", "/tmp/crux")
subprocess.call("chmod 755 /tmp/crux", shell=True)
index_files = ["auxlocs", "pepix", "protix"]
if not os.path.isdir("/tmp/fasta.index"):
os.mkdir("/tmp/fasta.index")
for index_file in index_files:
name = "{0:s}/{1:s}".format(species, index_file)
database.download(params["database_bucket"], name,
"/tmp/fasta.index/{0:s}".format(index_file))
output_dir = "/tmp/crux-output-{0:f}-{1:d}".format(
input_format["timestamp"], input_format["nonce"])
arguments = [
"--num-threads",
str(params["num_threads"]),
"--txt-output",
"T",
"--concat",
"T",
"--output-dir",
output_dir,
"--overwrite",
"T",
]
command = "cd /tmp; ./crux tide-search {0:s} fasta.index {1:s}".format(
file, " ".join(arguments))
try:
subprocess.check_output(command, stderr=subprocess.STDOUT, shell=True)
except subprocess.CalledProcessError as exc:
print("Status : FAIL", exc.returncode, exc.output)
raise exc
input_file = "{0:s}/tide-search.txt".format(output_dir)
output_format["suffix"] = species
output_format["ext"] = "txt"
output_file = "/tmp/{0:s}".format(util.file_name(output_format))
os.rename(input_file, output_file)
shutil.rmtree(output_dir)
return [output_file]
def run(database: Database, file: str, params, input_format, output_format):
database.download(params["database_bucket"], "crux", "/tmp/crux")
subprocess.call("chmod 755 /tmp/crux", shell=True)
command = "cd /tmp; ./crux param-medic {0:s}".format(file)
output = subprocess.check_output(command,
shell=True,
stderr=subprocess.STDOUT).decode("utf-8")
print(output)
phos = PHOSPHORYLATION.search(output)
itraq = ITRAQ.search(output)
silac = SILAC.search(output)
tmt6 = TMT6.search(output)
tmt10 = TMT10.search(output)
map_bucket = None
if tmt6:
if phos:
map_bucket = "maccoss-tmt6-phosphorylation-fasta"
else:
map_bucket = "maccoss-tmt6-fasta"
elif tmt10:
if phos:
map_bucket = "maccoss-tmt10-phosphorylation-fasta"
else:
map_bucket = "maccoss-tmt10-fasta"
elif itraq:
if phos:
map_bucket = "maccoss-itraq-phosphorylation-fasta"
else:
map_bucket = "maccoss-itraq-fasta"
elif phos:
map_bucket = "maccoss-phosphorylation-fasta"
elif silac:
map_bucket = "maccoss-silac-fasta"
else:
map_bucket = "maccoss-normal-fasta"
payload = {
"Records": [{
"s3": {
"bucket": {
"name": params["bucket"],
},
"object": {
"key": util.file_name(input_format),
},
"extra_params": {
"map_bucket": map_bucket,
"prefix": output_format["prefix"],
}
}
}]
}
output_file = util.file_name(output_format)
database.write(params["bucket"], output_file, output, {}, False)
database.invoke(params["output_function"], payload)
return []
