def aggregate(config):
setlogging(config, "aggregate")
'''
annotate(config)
Parameters
----------
config : dict
The config dict generated in the gomap.py script.
'''
from code.pipeline.run_argot2 import process_argot2, download_argot2
logging.info("Obtaining and aggregating Argot2.5 results")
download_argot2(config)
process_argot2(config)
from code.pipeline.mixed2gaf import mixed2gaf, filter_mixed
logging.info("Filtering mixed-method GAF")
mixed2gaf(config)
filter_mixed(config)
from code.pipeline.make_aggregate import clean_duplicate, clean_redundant, aggregate_datasets
logging.info("Cleaning and aggregating GAF files")
clean_duplicate(config)
clean_redundant(config)
aggregate_datasets(config)
def setup(config):
setlogging(config, "setup")
"""
setup(config)
This function downloads the **GOMAP-data.tar.gz** directory from CyVerse and extracts the content to the **data** directory. The steps run by this function is given below
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Parameters
----------
config : dict
The config dict generated in the gomap.py script.
"""
outdir = "data/"
cmd = ["irsync", "-rv", cyverse_path, outdir]
logging.info("Downloading file from Cyverse using irsync")
#The irsync will checksum the files on both ends and dtermine if the download is necessary and will only download if necessary
# might take time to check if the files needs to be downloaded
print(os.getcwd())
print(" ".join(cmd))
check_output_and_run("outfile", cmd)
with open("data/compress_files.txt", "r") as comp_files:
counter = 0
for infile in comp_files.readlines():
counter = counter + 1
outfile = outdir + infile.strip()
gzfile = outdir + infile.strip() + ".gz"
if os.path.exists(gzfile):
if os.path.exists(outfile):
print(gzfile + " already extracted")
else:
print("Extracting " + gzfile)
with gzip.open(gzfile, "rb") as in_f:
with open(outfile, "wb") as out_f:
shutil.copyfileobj(in_f, out_f)
os.remove(gzfile)
else:
print(gzfile + " doesn't exist")
with open("data/tar_files.txt", "r") as comp_files:
for infile in comp_files.readlines():
infile = infile.strip()
outfile = outdir + infile.strip()
tar_f = outdir + infile.strip() + ".tar.gz"
base_dir = os.path.basename(outfile)
if os.path.exists(tar_f):
if os.path.exists(outfile):
print(tar_f + " already extracted")
else:
print("Extracting " + tar_f)
with tarfile.open(tar_f) as tar:
tar.extractall("data/")
os.remove(tar_f)
else:
print(tar_f + " doesn't exist")
def init_dirs(config):
gomap_dir = config["input"]["workdir"] + "/GOMAP-" + config["input"][
"basename"]
config["input"]["gomap_dir"] = gomap_dir
if not os.path.exists(gomap_dir):
os.makedirs(gomap_dir, mode=0777)
excl_files = ['a']
for root, dir, files in os.walk(gomap_dir):
excl_files = excl_files + files
with open(config["pipeline"]["dir_struct"]) as tmp_file:
dir_struct = tmp_file.read()
with create_files(dir_struct) as workdir:
results = pyrocopy.copy(workdir,
gomap_dir,
excludeFiles=excl_files,
detailedResults=True)
setlogging(config, "init_dirs")
logging.info("Initializing directory structure")
logging.info(pformat(results))
return (config)
config = merger.merge(pipe_config, user_config)
config = init_dirs(config)
copy_input(config)
conf_out = config["input"]["gomap_dir"]+"/"+config["input"]["basename"]+".all.yml"
config["input"]["config_file"] = conf_out
with open(conf_out,"w") as out_f:
yaml.dump(config,out_f)
'''
Depending the step selected by the user we are going to run the relevant part of GO-MAP
'''
if main_args.step == "seqsim":
print("Running Sequence-similarity based Annotation Step")
setlogging(config,"seqsim")
logging.info("Running Sequence-similarity based Annotation Step")
run_seqsim(config)
elif main_args.step == "domain":
print("Running Domain Based Annotation Step")
setlogging(config,"domain")
logging.info("Running Domain Based Annotation Step")
run_domain(config)
elif main_args.step == "mixmeth-blast":
print("Running uniprot blast for mixed-methods")
setlogging(config,"mixmeth-preproc")
logging.info("Running uniprot blast for mixed-methods")
run_mixmeth_blast(config)
elif main_args.step == "mixmeth-preproc":
print("Running preprocessing step for mixed-methods")
setlogging(config,"mixmeth-preproc")