def main():
setup_logging()
args = parseOptions()
gtf_files = args.gtf_files.split(",")
fasta_files = args.fasta_files.split(",")
output_dir = args.output_dir
genome_build = args.genome_build
name = args.name
ver = args.version
tx_filter = args.filter
protein_map_file = args.protein_map_file
# create temp dir
tmpDir = tempfile.mkdtemp(prefix="onco_ensembl_ds_")
try:
logging.getLogger(__name__).info("Creating tmp dir (" + tmpDir + ") ....")
ds_build_dir = tmpDir + "/" + genome_build + "/"
os.mkdir(ds_build_dir)
if not (args.gtf_files.lower().find("gencode") !=-1) and tx_filter == "basic":
logging.getLogger(__name__).warn("basic filter requested for (apparently) a non-gencode set of GTFs. If this is an ENSEMBL run (not GENCODE), please specify dummy, using --filter.")
logging.getLogger(__name__).info("Creating config file...")
config_filename = ds_build_dir + "/" + name + ".config"
logging.getLogger(__name__).info("config file being written to: " + os.path.abspath(config_filename))
config_file_creator = GenericTsvDatasourceCreator()
idx_cols = DatasourceInstallUtils.indexCols("dummy_option", "dummy_values")
config_file_creator._createConfigFile(configFilename=config_filename + ".tmp", baseDSFile=os.path.basename(gtf_files[0]),ds_type="ensembl", ds_version=ver, ds_name=name, indexCols=idx_cols)
# Append the tx_filter and protein map file
config_parser = SafeConfigParser()
fp = file(config_filename + ".tmp", 'r')
config_parser.readfp(fp)
fp.close()
config_parser.set("general", "transcript_filter", tx_filter)
# Write updated config file
fp = file(config_filename, 'w')
config_parser.write(fp)
fp.close()
logging.getLogger(__name__).info("Starting index construction (temp location: " + ds_build_dir + ") ...")
factory = GenomeBuildFactory()
factory.construct_ensembl_indices(gtf_files, fasta_files, ds_build_dir + os.path.basename(gtf_files[0]), protein_id_mapping_file=protein_map_file)
logging.getLogger(__name__).info("Creating datasource md5...")
DatasourceInstallUtils.create_datasource_md5_file(ds_build_dir)
logging.getLogger(__name__).info("Copying created datasource from temp directory to final location (" + output_dir + ")...")
shutil.copytree(symlinks=True, src=tmpDir, dst=output_dir)
except Exception as e:
import traceback
logging.getLogger(__name__).fatal((e.__repr__()) + " " + traceback.format_exc())
logging.getLogger(__name__).info(""""If you are getting and error such as: KeyError: 'ENST00000474204.1'), then you may be out of disk space in /tmp/.""")
# Remove the tempdir
logging.getLogger(__name__).info("Done...")
logging.getLogger(__name__).info("Removing ..." + tmpDir + '/')
shutil.rmtree(tmpDir)
