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)