def functionalAnnotSeed(infile, outfile):
job_memory = str(PARAMS["Eggnogmapper_memory"]) + "G"
job_threads = int(PARAMS["Eggnogmapper_threads"])
#generate call to eggnog-mapper
#requires older version of diamond to use the eggnog mapper databases
statement = "module load bio/diamond/0.8.22 && "
statement += PipelineAnnotate.runEggmapSeed(infile, infile, PARAMS)
P.run(statement)
def functionalAnnotSeed(infile, outfile):
job_memory = str(PARAMS["Eggnogmapper_memory"]) + "G"
job_threads = int(PARAMS["Eggnogmapper_threads"])
#generate call to eggnog-mapper
#option to add commands to load specific versions of diamond and python2 etc. if needed
if PARAMS["Eggnogmapper_preload"] not in ["", "false"]:
statement = "{} &&".format(PARAMS["Eggnogmapper_preload"])
else:
statement = ""
statement += PipelineAnnotate.runEggmapSeed(infile.replace(".log", ""),
infile.replace(".log", ""),
PARAMS)
statement += ' && echo "Made file {}." > {}'.format(
outfile.replace(".log", ""), outfile)
P.run(statement)