def functionalAnnotChunks(infile, outfile):
job_memory = str(PARAMS["Eggnogmapper_memory_annot"]) + "G"
job_threads = int(str(PARAMS["Eggnogmapper_threads_annot"]))
statement = []
if PARAMS["Eggnogmapper_scratch"] == "true":
#copy the db into fast local SSD
statement.append("cp {}eggnog.db $SCRATCH_DIR/eggnog.db".format(
PARAMS["Eggnogmapper_eggdata"]))
datadir = "$SCRATCH_DIR"
else:
datadir = PARAMS["Eggnogmapper_eggdata"]
#get annotation from seeds
statement.append(
PipelineAnnotate.runEggmapAnnot(
infile, outfile.replace(".emapper.annotations", ""), PARAMS,
datadir))
statement = " && ".join(statement)
#run the annotation step
P.run(statement)
def functionalAnnotChunks(infile, outfile):
job_memory = str(PARAMS["Eggnogmapper_memory_annot"]) + "G"
job_threads = int(str(PARAMS["Eggnogmapper_threads_annot"]))
statement = []
#option to add commands to load specific versions of diamond and python2 etc. if needed
if PARAMS["Eggnogmapper_preload"] not in ["", "false"]:
statement.append("{}".format(PARAMS["Eggnogmapper_preload"]))
if PARAMS["Eggnogmapper_scratch"] == "true":
#copy the db into fast local SSD
statement.append("cp {}eggnog.db $SCRATCH_DIR/eggnog.db".format(
PARAMS["Eggnogmapper_eggdata"]))
datadir = "$SCRATCH_DIR"
else:
datadir = PARAMS["Eggnogmapper_eggdata"]
#get annotation from seeds
statement.append(
PipelineAnnotate.runEggmapAnnot(
infile.replace(".log", ""),
outfile.replace(".emapper.annotations.log", ""), PARAMS, datadir))
statement.append('echo "Made file {}." > {}'.format(
outfile.replace(".log", ""), outfile))
statement = " && ".join(statement)
#run the annotation step
P.run(statement)