fof = sys.argv[1] version = sys.argv[2] sampleid = sys.argv[3] except: sys.exit(sys.argv[0] + " <focus output file that ONLY has taxon [tab] percent> <version (any string)> <sampleid (any string)>") # read FOCUS results count={} with open(fof, 'r') as gin: for l in gin: p=l.strip().split("\t") count[p[0].strip()]=float(p[1]) # read our pickled data data = load_pickle("/home3/redwards/Cami_Challenge/edwardslab_CAMI/redwards/python/taxonomy.p") # now we need to go through all levels and sum the results levels = {} parent_tax = {} # print the header information # print("#CAMI Submission for Taxonomic Profiling") print("@Version:0.9.2") # not supported despite documentation #print("@_DATABASE_:" + version) print("@SampleID:"+ sampleid)
fof = sys.argv[1] version = sys.argv[2] sampleid = sys.argv[3] except: sys.exit(sys.argv[0] + " <focus output file that ONLY has taxon [tab] percent> <version (any string)> <sampleid (any string)>") # read FOCUS results count={} with open(fof, 'r') as gin: for l in gin: p=l.strip().split("\t") count[p[0].strip()]=float(p[1]) # read our pickled data data = load_pickle() # now we need to go through all levels and sum the results levels = {} parent_tax = {} # print the header information # print("#CAMI Submission for Taxonomic Profiling") print("@Version:" + version) print("@SampleID:"+ sampleid) print("@Ranks:superkingdom|phylum|class|order|family|genus|species|strain\n")