def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
# setup command line parser
parser = E.OptionParser(version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option("-s",
"--summarise",
dest="summarise",
type="choice",
choices=("level-counts", "taxa-counts", "individual"),
help="summarise the taxa counts - no. phyla etc")
parser.add_option("--output-map",
dest="output_map",
action="store_true",
help="ouput map of taxonomy")
# add common options (-h/--help, ...) and parse command line
(options, args) = E.Start(parser, argv=argv)
if options.output_map:
found = []
options.stdout.write("""Domain\t \
kingdom\t \
phylum\t \
class\t \
order\t \
family\t \
genus\t \
species\n""")
# only output the mapping file - do not continue
# summarise regardless of the specified options
for lca in LCA.iterate(options.stdin):
# if bacteria or archaea the kingdom will
# be the domain
if lca.domain == "Bacteria" or lca.domain == "Archaea":
kingdom = lca.domain
else:
kingdom = lca.kingdom
hierarchy = [
lca.domain, kingdom, lca.phylum, lca._class, lca.order,
lca.family, lca.genus, lca.species
]
if hierarchy in found:
continue
else:
found.append(hierarchy)
options.stdout.write("\t".join(hierarchy) + "\n")
return
if options.summarise == "level-counts":
level_counts = collections.defaultdict(set)
total = 0
nreads_domain = 0
nreads_kingdom = 0
nreads_kingdom_plus = 0
nreads_phylum = 0
nreads_phylum_plus = 0
nreads_class = 0
nreads_class_plus = 0
nreads_order = 0
nreads_order_plus = 0
nreads_family = 0
nreads_family_plus = 0
nreads_genus = 0
nreads_genus_plus = 0
nreads_species = 0
nreads_species_plus = 0
nreads_subspecies = 0
nreads_subspecies_plus = 0
c = E.Counter()
for lca in LCA.iterate(options.stdin):
total += 1
if lca.domain != "NA":
nreads_domain += 1
level_counts["domain"].add(lca.domain)
else:
c.kingdom_unmapped += 1
if lca.kingdom != "NA":
nreads_kingdom += 1
level_counts["kingdom"].add(lca.kingdom)
else:
c.kingdom_unmapped += 1
if lca.kingdom_plus != "NA":
nreads_kingdom_plus += 1
level_counts["kingdom+"].add(lca.kingdom_plus)
else:
c.kingdom_plus_unmapped += 1
if lca.phylum != "NA":
nreads_phylum += 1
level_counts["phylum"].add(lca.phylum)
else:
c.phylum_unmapped += 1
if lca.phylum_plus != "NA":
nreads_phylum_plus += 1
level_counts["phylum+"].add(lca.phylum_plus)
else:
c.phylum_plus_unmapped += 1
if lca._class != "NA":
nreads_class += 1
level_counts["class"].add(lca._class)
else:
c.class_unmapped += 1
if lca._class_plus != "NA":
nreads_class_plus += 1
level_counts["class+"].add(lca._class_plus)
else:
c.class_plus_unmapped += 1
if lca.order != "NA":
nreads_order += 1
level_counts["order"].add(lca.order)
else:
c.order_unmapped += 1
if lca.order_plus != "NA":
nreads_order_plus += 1
level_counts["order+"].add(lca.order_plus)
else:
c.order_plus_unmapped += 1
if lca.family != "NA":
nreads_family += 1
level_counts["family"].add(lca.family)
else:
c.family_unmapped += 1
if lca.family != "NA":
nreads_family_plus == 1
level_counts["family+"].add(lca.family_plus)
else:
c.family_plus_unmapped += 1
if lca.genus != "NA":
nreads_genus += 1
level_counts["genus"].add(lca.genus)
else:
c.genus_unmapped += 1
if lca.genus_plus != "NA":
nreads_genus_plus == 1
level_counts["genus+"].add(lca.genus_plus)
else:
c.genus_plus_unmapped += 1
if lca.species != "NA":
nreads_species += 1
level_counts["species"].add(lca.species)
else:
c.species_unmapped += 1
if lca.species_plus != "NA":
nreads_species_plus += 1
level_counts["species+"].add(lca.species_plus)
else:
c.species_plus_unmapped += 1
# removed subspecies mapping for the time
# being
# if lca.subspecies != "NA":
# nreads_subspecies += 1
# level_counts["subspecies"].add(lca.subspecies)
# else:
# c.subspecies_unmapped += 1
# if lca.subspecies_plus != "NA":
# nreads_subspecies_plus += 1
# level_counts["subspecies+"].add(lca.subspecies_plus)
# else:
# c.subspecies_plus_unmapped += 1
options.stdout.write("\t".join([
"ndomain", "nkingdom", "nkingdom+", "nphylum", "nphylum+",
"nclass", "nclass+", "norder", "norder+", "nfamily", "nfamily+",
"ngenus", "ngenus+", "nspecies", "nspecies+", "nseqkingdom",
"nseqkingdom+", "nseqphylum", "nseqphylum+", "nseqclass",
"nseqclass+", "nseqorder", "nseqorder+", "nseqfamily",
"nseqfamily+", "nseqgenus", "nseqgenus+", "nseqspecies",
"nseqspecies+"
]) + "\n")
options.stdout.write("\t".join(
map(str, [
len(level_counts["domain"]),
len(level_counts["kingdom"]),
len(level_counts["kingdom+"]),
len(level_counts["phylum"]),
len(level_counts["phylum+"]),
len(level_counts["class"]),
len(level_counts["class+"]),
len(level_counts["order"]),
len(level_counts["order+"]),
len(level_counts["family"]),
len(level_counts["family+"]),
len(level_counts["genus"]),
len(level_counts["genus+"]),
len(level_counts["species"]),
len(level_counts["species+"]), nreads_domain, nreads_kingdom,
nreads_phylum, nreads_phylum_plus, nreads_class,
nreads_class_plus, nreads_order, nreads_order_plus,
nreads_family, nreads_family_plus, nreads_genus,
nreads_genus_plus, nreads_species, nreads_species_plus
])) + "\n")
elif options.summarise == "taxa-counts":
unmapped = collections.defaultdict(int)
total = 0
taxa_counts = {
"domain": collections.defaultdict(int),
"kingdom": collections.defaultdict(int),
"kingdom+": collections.defaultdict(int),
"phylum": collections.defaultdict(int),
"phylum+": collections.defaultdict(int),
"class": collections.defaultdict(int),
"class+": collections.defaultdict(int),
"order": collections.defaultdict(int),
"order+": collections.defaultdict(int),
"family": collections.defaultdict(int),
"family+": collections.defaultdict(int),
"genus": collections.defaultdict(int),
"genus+": collections.defaultdict(int),
"species": collections.defaultdict(int),
"species+": collections.defaultdict(int)
}
c = E.Counter()
for lca in LCA.iterate(options.stdin):
total += 1
if lca.domain != "NA":
taxa_counts["domain"][lca.domain] += 1
else:
c.kingdom_unmapped += 1
unmapped["domain"] += 1
if lca.kingdom != "NA":
taxa_counts["kingdom"][lca.kingdom] += 1
else:
c.kingdom_unmapped += 1
unmapped["kingdom"] += 1
if lca.kingdom_plus != "NA":
taxa_counts["kingdom+"][lca.kingdom_plus] += 1
else:
c.kingdom_plus_unmapped += 1
unmapped["kingdom+"] += 1
if lca.phylum != "NA":
taxa_counts["phylum"][lca.phylum] += 1
else:
c.phylum_unmapped += 1
unmapped["phylum"] += 1
if lca.phylum_plus != "NA":
taxa_counts["phylum+"][lca.phylum_plus] += 1
else:
c.phylum_plus_unmapped += 1
unmapped["phylum+"] += 1
if lca._class != "NA":
taxa_counts["class"][lca._class] += 1
else:
c.class_unmapped += 1
unmapped["class"] += 1
if lca._class_plus != "NA":
taxa_counts["class+"][lca._class_plus] += 1
else:
c.class_plus_unmapped += 1
unmapped["class+"] += 1
if lca.order != "NA":
taxa_counts["order"][lca.order] += 1
else:
c.order_unmapped += 1
unmapped["order"] += 1
if lca.order_plus != "NA":
taxa_counts["order+"][lca.order_plus] += 1
else:
c.order_plus_unmapped += 1
unmapped["order+"] += 1
if lca.family != "NA":
taxa_counts["family"][lca.family] += 1
else:
c.family_unmapped += 1
unmapped["family"] += 1
if lca.family_plus != "NA":
taxa_counts["family+"][lca.family_plus] += 1
else:
c.family_plus_unmapped += 1
unmapped["family+"] += 1
if lca.genus != "NA":
taxa_counts["genus"][lca.genus] += 1
else:
c.genus_unmapped += 1
unmapped["genus"] += 1
if lca.genus_plus != "NA":
taxa_counts["genus+"][lca.genus_plus] += 1
else:
c.genus_plus_unmapped += 1
unmapped["genus+"] += 1
if lca.species != "NA":
taxa_counts["species"][lca.species] += 1
else:
c.species_unmapped += 1
unmapped["species"] += 1
if lca.species_plus != "NA":
taxa_counts["species+"][lca.species_plus] += 1
else:
c.species_plus_unmapped += 1
unmapped["species+"] += 1
options.stdout.write("level\ttaxa\tcount\tproportion\trpm\n")
for level, taxa_count in sorted(taxa_counts.items()):
total_level = total - unmapped[level]
for taxa, count in sorted(taxa_count.items()):
options.stdout.write("\t".join([
level, taxa,
str(count), "{:.8}".format(float(count) /
total_level), "{:.8}".
format(float(count) / (float(total_level) / 1000000))
]) + "\n")
E.info(c)
elif options.summarise == "individual":
# each read is output with its respective
# taxon assignments
options.stdout.write("\t".join([
"id", "domain", "kingdom", "kingdom+", "phylum", "phylum+",
"class", "class+", "order", "order+", "family", "family+", "genus",
"genus+", "species", "species+"
]) + "\n")
for lca in LCA.iterate(options.stdin):
options.stdout.write("\t".join([
lca.identifier, lca.domain, lca.kingdom, lca.kingdom_plus,
lca.phylum, lca.phylum_plus, lca._class, lca._class_plus,
lca.order, lca.order_plus, lca.family, lca.family_plus,
lca.genus, lca.genus_plus, lca.species, lca.species_plus
]) + "\n")
# write footer and output benchmark information.
E.Stop()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
# setup command line parser
parser = E.OptionParser(version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option("-s", "--summarise", dest="summarise", type="choice",
choices=("level-counts", "taxa-counts", "individual"),
help="summarise the taxa counts - no. phyla etc")
parser.add_option("--output-map", dest="output_map", action="store_true",
help="ouput map of taxonomy")
# add common options (-h/--help, ...) and parse command line
(options, args) = E.Start(parser, argv=argv)
if options.output_map:
found = []
options.stdout.write("""Domain\t \
kingdom\t \
phylum\t \
class\t \
order\t \
family\t \
genus\t \
species\n""")
# only output the mapping file - do not continue
# summarise regardless of the specified options
for lca in LCA.iterate(options.stdin):
# if bacteria or archaea the kingdom will
# be the domain
if lca.domain == "Bacteria" or lca.domain == "Archaea":
kingdom = lca.domain
else:
kingdom = lca.kingdom
hierarchy = [lca.domain,
kingdom,
lca.phylum,
lca._class,
lca.order,
lca.family,
lca.genus,
lca.species]
if hierarchy in found:
continue
else:
found.append(hierarchy)
options.stdout.write("\t".join(hierarchy) + "\n")
return
if options.summarise == "level-counts":
level_counts = collections.defaultdict(set)
total = 0
nreads_domain = 0
nreads_kingdom = 0
nreads_kingdom_plus = 0
nreads_phylum = 0
nreads_phylum_plus = 0
nreads_class = 0
nreads_class_plus = 0
nreads_order = 0
nreads_order_plus = 0
nreads_family = 0
nreads_family_plus = 0
nreads_genus = 0
nreads_genus_plus = 0
nreads_species = 0
nreads_species_plus = 0
nreads_subspecies = 0
nreads_subspecies_plus = 0
c = E.Counter()
for lca in LCA.iterate(options.stdin):
total += 1
if lca.domain != "NA":
nreads_domain += 1
level_counts["domain"].add(lca.domain)
else:
c.kingdom_unmapped += 1
if lca.kingdom != "NA":
nreads_kingdom += 1
level_counts["kingdom"].add(lca.kingdom)
else:
c.kingdom_unmapped += 1
if lca.kingdom_plus != "NA":
nreads_kingdom_plus += 1
level_counts["kingdom+"].add(lca.kingdom_plus)
else:
c.kingdom_plus_unmapped += 1
if lca.phylum != "NA":
nreads_phylum += 1
level_counts["phylum"].add(lca.phylum)
else:
c.phylum_unmapped += 1
if lca.phylum_plus != "NA":
nreads_phylum_plus += 1
level_counts["phylum+"].add(lca.phylum_plus)
else:
c.phylum_plus_unmapped += 1
if lca._class != "NA":
nreads_class += 1
level_counts["class"].add(lca._class)
else:
c.class_unmapped += 1
if lca._class_plus != "NA":
nreads_class_plus += 1
level_counts["class+"].add(lca._class_plus)
else:
c.class_plus_unmapped += 1
if lca.order != "NA":
nreads_order += 1
level_counts["order"].add(lca.order)
else:
c.order_unmapped += 1
if lca.order_plus != "NA":
nreads_order_plus += 1
level_counts["order+"].add(lca.order_plus)
else:
c.order_plus_unmapped += 1
if lca.family != "NA":
nreads_family += 1
level_counts["family"].add(lca.family)
else:
c.family_unmapped += 1
if lca.family != "NA":
nreads_family_plus == 1
level_counts["family+"].add(lca.family_plus)
else:
c.family_plus_unmapped += 1
if lca.genus != "NA":
nreads_genus += 1
level_counts["genus"].add(lca.genus)
else:
c.genus_unmapped += 1
if lca.genus_plus != "NA":
nreads_genus_plus == 1
level_counts["genus+"].add(lca.genus_plus)
else:
c.genus_plus_unmapped += 1
if lca.species != "NA":
nreads_species += 1
level_counts["species"].add(lca.species)
else:
c.species_unmapped += 1
if lca.species_plus != "NA":
nreads_species_plus += 1
level_counts["species+"].add(lca.species_plus)
else:
c.species_plus_unmapped += 1
# removed subspecies mapping for the time
# being
# if lca.subspecies != "NA":
# nreads_subspecies += 1
# level_counts["subspecies"].add(lca.subspecies)
# else:
# c.subspecies_unmapped += 1
# if lca.subspecies_plus != "NA":
# nreads_subspecies_plus += 1
# level_counts["subspecies+"].add(lca.subspecies_plus)
# else:
# c.subspecies_plus_unmapped += 1
options.stdout.write("\t".join(["ndomain",
"nkingdom",
"nkingdom+",
"nphylum",
"nphylum+",
"nclass",
"nclass+",
"norder",
"norder+",
"nfamily",
"nfamily+",
"ngenus",
"ngenus+",
"nspecies",
"nspecies+",
"nseqkingdom",
"nseqkingdom+",
"nseqphylum",
"nseqphylum+",
"nseqclass",
"nseqclass+",
"nseqorder",
"nseqorder+",
"nseqfamily",
"nseqfamily+",
"nseqgenus",
"nseqgenus+",
"nseqspecies",
"nseqspecies+"]) + "\n")
options.stdout.write("\t".join(map(
str, [len(level_counts["domain"]),
len(level_counts["kingdom"]),
len(level_counts["kingdom+"]),
len(level_counts["phylum"]),
len(level_counts["phylum+"]),
len(level_counts["class"]),
len(level_counts["class+"]),
len(level_counts["order"]),
len(level_counts["order+"]),
len(level_counts["family"]),
len(level_counts["family+"]),
len(level_counts["genus"]),
len(level_counts["genus+"]),
len(level_counts["species"]),
len(level_counts["species+"]),
nreads_domain,
nreads_kingdom,
nreads_phylum,
nreads_phylum_plus,
nreads_class,
nreads_class_plus,
nreads_order,
nreads_order_plus,
nreads_family,
nreads_family_plus,
nreads_genus,
nreads_genus_plus,
nreads_species,
nreads_species_plus])) + "\n")
elif options.summarise == "taxa-counts":
unmapped = collections.defaultdict(int)
total = 0
taxa_counts = {"domain": collections.defaultdict(int),
"kingdom": collections.defaultdict(int),
"kingdom+": collections.defaultdict(int),
"phylum": collections.defaultdict(int),
"phylum+": collections.defaultdict(int),
"class": collections.defaultdict(int),
"class+": collections.defaultdict(int),
"order": collections.defaultdict(int),
"order+": collections.defaultdict(int),
"family": collections.defaultdict(int),
"family+": collections.defaultdict(int),
"genus": collections.defaultdict(int),
"genus+": collections.defaultdict(int),
"species": collections.defaultdict(int),
"species+": collections.defaultdict(int)}
c = E.Counter()
for lca in LCA.iterate(options.stdin):
total += 1
if lca.domain != "NA":
taxa_counts["domain"][lca.domain] += 1
else:
c.kingdom_unmapped += 1
unmapped["domain"] += 1
if lca.kingdom != "NA":
taxa_counts["kingdom"][lca.kingdom] += 1
else:
c.kingdom_unmapped += 1
unmapped["kingdom"] += 1
if lca.kingdom_plus != "NA":
taxa_counts["kingdom+"][lca.kingdom_plus] += 1
else:
c.kingdom_plus_unmapped += 1
unmapped["kingdom+"] += 1
if lca.phylum != "NA":
taxa_counts["phylum"][lca.phylum] += 1
else:
c.phylum_unmapped += 1
unmapped["phylum"] += 1
if lca.phylum_plus != "NA":
taxa_counts["phylum+"][lca.phylum_plus] += 1
else:
c.phylum_plus_unmapped += 1
unmapped["phylum+"] += 1
if lca._class != "NA":
taxa_counts["class"][lca._class] += 1
else:
c.class_unmapped += 1
unmapped["class"] += 1
if lca._class_plus != "NA":
taxa_counts["class+"][lca._class_plus] += 1
else:
c.class_plus_unmapped += 1
unmapped["class+"] += 1
if lca.order != "NA":
taxa_counts["order"][lca.order] += 1
else:
c.order_unmapped += 1
unmapped["order"] += 1
if lca.order_plus != "NA":
taxa_counts["order+"][lca.order_plus] += 1
else:
c.order_plus_unmapped += 1
unmapped["order+"] += 1
if lca.family != "NA":
taxa_counts["family"][lca.family] += 1
else:
c.family_unmapped += 1
unmapped["family"] += 1
if lca.family_plus != "NA":
taxa_counts["family+"][lca.family_plus] += 1
else:
c.family_plus_unmapped += 1
unmapped["family+"] += 1
if lca.genus != "NA":
taxa_counts["genus"][lca.genus] += 1
else:
c.genus_unmapped += 1
unmapped["genus"] += 1
if lca.genus_plus != "NA":
taxa_counts["genus+"][lca.genus_plus] += 1
else:
c.genus_plus_unmapped += 1
unmapped["genus+"] += 1
if lca.species != "NA":
taxa_counts["species"][lca.species] += 1
else:
c.species_unmapped += 1
unmapped["species"] += 1
if lca.species_plus != "NA":
taxa_counts["species+"][lca.species_plus] += 1
else:
c.species_plus_unmapped += 1
unmapped["species+"] += 1
options.stdout.write("level\ttaxa\tcount\tproportion\trpm\n")
for level, taxa_count in sorted(taxa_counts.items()):
total_level = total - unmapped[level]
for taxa, count in sorted(taxa_count.items()):
options.stdout.write("\t".join(
[level,
taxa,
str(count),
"{:.8}".format(float(count)/total_level),
"{:.8}".format(float(count)/(float(total_level)/1000000))])
+ "\n")
E.info(c)
elif options.summarise == "individual":
# each read is output with its respective
# taxon assignments
options.stdout.write("\t".join(["id",
"domain",
"kingdom",
"kingdom+",
"phylum",
"phylum+",
"class",
"class+",
"order",
"order+",
"family",
"family+",
"genus",
"genus+",
"species",
"species+"]) + "\n")
for lca in LCA.iterate(options.stdin):
options.stdout.write("\t".join([lca.identifier,
lca.domain,
lca.kingdom,
lca.kingdom_plus,
lca.phylum,
lca.phylum_plus,
lca._class,
lca._class_plus,
lca.order,
lca.order_plus,
lca.family,
lca.family_plus,
lca.genus,
lca.genus_plus,
lca.species,
lca.species_plus]) + "\n")
# write footer and output benchmark information.
E.Stop()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv == None: argv = sys.argv
# setup command line parser
parser = E.OptionParser(version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option(
"-s",
"--summarise",
dest="summarise",
type="choice",
choices=("level-counts", "taxa-counts", "individual"),
help="summarise the taxa counts i.e. no. phyla, classes etc")
## add common options (-h/--help, ...) and parse command line
(options, args) = E.Start(parser, argv=argv)
if options.summarise == "level-counts":
level_counts = collections.defaultdict(set)
total = 0
nreads_kingdom = 0
nreads_kingdom_plus = 0
nreads_phylum = 0
nreads_phylum_plus = 0
nreads_class = 0
nreads_class_plus = 0
nreads_order = 0
nreads_order_plus = 0
nreads_family = 0
nreads_family_plus = 0
nreads_genus = 0
nreads_genus_plus = 0
nreads_species = 0
nreads_species_plus = 0
nreads_subspecies = 0
nreads_subspecies_plus = 0
c = E.Counter()
for lca in LCA.iterate(options.stdin):
total += 1
if lca.kingdom != "NA":
nreads_kingdom += 1
level_counts["kingdom"].add(lca.kingdom)
else:
c.kingdom_unmapped += 1
if lca.kingdom_plus != "NA":
nreads_kingdom_plus += 1
level_counts["kingdom+"].add(lca.kingdom_plus)
else:
c.kingdom_plus_unmapped += 1
if lca.phylum != "NA":
nreads_phylum += 1
level_counts["phylum"].add(lca.phylum)
else:
c.phylum_unmapped += 1
if lca.phylum_plus != "NA":
nreads_phylum_plus += 1
level_counts["phylum+"].add(lca.phylum_plus)
else:
c.phylum_plus_unmapped += 1
if lca._class != "NA":
nreads_class += 1
level_counts["class"].add(lca._class)
else:
c.class_unmapped += 1
if lca._class_plus != "NA":
nreads_class_plus += 1
level_counts["class+"].add(lca._class_plus)
else:
c.class_plus_unmapped += 1
if lca.order != "NA":
nreads_order += 1
level_counts["order"].add(lca.order)
else:
c.order_unmapped += 1
if lca.order_plus != "NA":
nreads_order_plus += 1
level_counts["order+"].add(lca.order_plus)
else:
c.order_plus_unmapped += 1
if lca.family != "NA":
nreads_family += 1
level_counts["family"].add(lca.family)
else:
c.family_unmapped += 1
if lca.family != "NA":
nreads_family_plus == 1
level_counts["family+"].add(lca.family_plus)
else:
c.family_plus_unmapped += 1
if lca.genus != "NA":
nreads_genus += 1
level_counts["genus"].add(lca.genus)
else:
c.genus_unmapped += 1
if lca.genus_plus != "NA":
nreads_genus_plus == 1
level_counts["genus+"].add(lca.genus_plus)
else:
c.genus_plus_unmapped += 1
if lca.species != "NA":
nreads_species += 1
level_counts["species"].add(lca.species)
else:
c.species_unmapped += 1
if lca.species_plus != "NA":
nreads_species_plus += 1
level_counts["species+"].add(lca.species_plus)
else:
c.species_plus_unmapped += 1
if lca.subspecies != "NA":
nreads_subspecies += 1
level_counts["subspecies"].add(lca.subspecies)
else:
c.subspecies_unmapped += 1
if lca.subspecies_plus != "NA":
nreads_subspecies_plus += 1
level_counts["subspecies+"].add(lca.subspecies_plus)
else:
c.subspecies_plus_unmapped += 1
options.stdout.write("\t".join([
"nkingdom", "nkingdom+", "nphylum", "nphylum+", "nclass",
"nclass+", "norder", "norder+", "nfamily", "nfamily+", "ngenus",
"ngenus+", "nspecies", "nspecies+", "nsubspecies", "nsubspecies+",
"nseqkingdom", "nseqkingdom+", "nseqphylum", "nseqphylum+",
"nseqclass", "nseqclass+", "nseqorder", "nseqorder+", "nseqfamily",
"nseqfamily+", "nseqgenus", "nseqgenus+", "nseqspecies",
"nseqspecies+", "nseqsubspecies", "nseqsubspecies+"
]) + "\n")
options.stdout.write("\t".join(
map(str, [
len(level_counts["kingdom"]),
len(level_counts["kingdom+"]),
len(level_counts["phylum"]),
len(level_counts["phylum+"]),
len(level_counts["class"]),
len(level_counts["class+"]),
len(level_counts["order"]),
len(level_counts["order+"]),
len(level_counts["family"]),
len(level_counts["family+"]),
len(level_counts["genus"]),
len(level_counts["genus+"]),
len(level_counts["species"]),
len(level_counts["species+"]),
len(level_counts["subspecies"]),
len(level_counts["subspecies+"]), nreads_kingdom,
nreads_phylum, nreads_phylum_plus, nreads_class,
nreads_class_plus, nreads_order, nreads_order_plus,
nreads_family, nreads_family_plus, nreads_genus,
nreads_genus_plus, nreads_species, nreads_species_plus,
nreads_subspecies, nreads_subspecies_plus
])) + "\n")
elif options.summarise == "taxa-counts":
unmapped = collections.defaultdict(int)
total = 0
taxa_counts = {
"kingdom": collections.defaultdict(int),
"kingdom+": collections.defaultdict(int),
"phylum": collections.defaultdict(int),
"phylum+": collections.defaultdict(int),
"class": collections.defaultdict(int),
"class+": collections.defaultdict(int),
"order": collections.defaultdict(int),
"order+": collections.defaultdict(int),
"family": collections.defaultdict(int),
"family+": collections.defaultdict(int),
"genus": collections.defaultdict(int),
"genus+": collections.defaultdict(int),
"species": collections.defaultdict(int),
"species+": collections.defaultdict(int),
"subspecies": collections.defaultdict(int),
"subspecies+": collections.defaultdict(int)
}
c = E.Counter()
for lca in LCA.iterate(options.stdin):
total += 1
if lca.kingdom != "NA":
taxa_counts["kingdom"][lca.kingdom] += 1
else:
c.kingdom_unmapped += 1
unmapped["kingdom"] += 1
if lca.kingdom_plus != "NA":
taxa_counts["kingdom+"][lca.kingdom_plus] += 1
else:
c.kingdom_plus_unmapped += 1
unmapped["kingdom+"] += 1
if lca.phylum != "NA":
taxa_counts["phylum"][lca.phylum] += 1
else:
c.phylum_unmapped += 1
unmapped["phylum"] += 1
if lca.phylum_plus != "NA":
taxa_counts["phylum+"][lca.phylum_plus] += 1
else:
c.phylum_plus_unmapped += 1
unmapped["phylum+"] += 1
if lca._class != "NA":
taxa_counts["class"][lca._class] += 1
else:
c.class_unmapped += 1
unmapped["class"] += 1
if lca._class_plus != "NA":
taxa_counts["class+"][lca._class_plus] += 1
else:
c.class_plus_unmapped += 1
unmapped["class+"] += 1
if lca.order != "NA":
taxa_counts["order"][lca.order] += 1
else:
c.order_unmapped += 1
unmapped["order"] += 1
if lca.order_plus != "NA":
taxa_counts["order+"][lca.order_plus] += 1
else:
c.order_plus_unmapped += 1
unmapped["order+"] += 1
if lca.family != "NA":
taxa_counts["family"][lca.family] += 1
else:
c.family_unmapped += 1
unmapped["family"] += 1
if lca.family_plus != "NA":
taxa_counts["family+"][lca.family_plus] += 1
else:
c.family_plus_unmapped += 1
unmapped["family+"] += 1
if lca.genus != "NA":
taxa_counts["genus"][lca.genus] += 1
else:
c.genus_unmapped += 1
unmapped["genus"] += 1
if lca.genus_plus != "NA":
taxa_counts["genus+"][lca.genus_plus] += 1
else:
c.genus_plus_unmapped += 1
unmapped["genus+"] += 1
if lca.species != "NA":
taxa_counts["species"][lca.species] += 1
else:
c.species_unmapped += 1
unmapped["species"] += 1
if lca.species_plus != "NA":
taxa_counts["species+"][lca.species_plus] += 1
else:
c.species_plus_unmapped += 1
unmapped["species+"] += 1
if lca.subspecies != "NA":
taxa_counts["subspecies"][lca.subspecies] += 1
else:
c.subspecies_unmapped += 1
unmapped["subspecies"] += 1
if lca.subspecies_plus != "NA":
taxa_counts["subspecies+"][lca.subspecies_plus] += 1
else:
c.subspecies_plus_unmapped += 1
unmapped["subspecies+"] += 1
options.stdout.write("level\ttaxa\tcount\tproportion\n")
for level, taxa_count in taxa_counts.iteritems():
total_level = total - unmapped[level]
for taxa, count in taxa_count.iteritems():
options.stdout.write("\t".join(
[level, taxa,
str(count),
str(float(count) / total_level)]) + "\n")
E.info(c)
elif options.summarise == "individual":
# each read is output with its respective
# taxon assignments
options.stdout.write("\t".join([
"id", "kingdom", "kingdom+", "phylum", "phylum+", "class",
"class+", "order", "order+", "family", "family+", "genus",
"genus+", "species", "species+", "subspecies", "subspecies+"
]) + "\n")
for lca in LCA.iterate(options.stdin):
options.stdout.write("\t".join([
lca.identifier, lca.kingdom, lca.kingdom_plus, lca.phylum,
lca.phylum_plus, lca._class, lca._class_plus, lca.order,
lca.order_plus, lca.family, lca.family_plus, lca.genus,
lca.genus_plus, lca.species, lca.species_plus, lca.subspecies,
lca.subspecies_plus
]) + "\n")
## write footer and output benchmark information.
E.Stop()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv == None:
argv = sys.argv
# setup command line parser
parser = E.OptionParser(version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option("-s", "--summarise", dest="summarise", type="choice", choices=("level-counts",
"taxa-counts", "individual"), help="summarise the taxa counts i.e. no. phyla, classes etc")
# add common options (-h/--help, ...) and parse command line
(options, args) = E.Start(parser, argv=argv)
if options.summarise == "level-counts":
level_counts = collections.defaultdict(set)
total = 0
nreads_kingdom = 0
nreads_kingdom_plus = 0
nreads_phylum = 0
nreads_phylum_plus = 0
nreads_class = 0
nreads_class_plus = 0
nreads_order = 0
nreads_order_plus = 0
nreads_family = 0
nreads_family_plus = 0
nreads_genus = 0
nreads_genus_plus = 0
nreads_species = 0
nreads_species_plus = 0
nreads_subspecies = 0
nreads_subspecies_plus = 0
c = E.Counter()
for lca in LCA.iterate(options.stdin):
total += 1
if lca.kingdom != "NA":
nreads_kingdom += 1
level_counts["kingdom"].add(lca.kingdom)
else:
c.kingdom_unmapped += 1
if lca.kingdom_plus != "NA":
nreads_kingdom_plus += 1
level_counts["kingdom+"].add(lca.kingdom_plus)
else:
c.kingdom_plus_unmapped += 1
if lca.phylum != "NA":
nreads_phylum += 1
level_counts["phylum"].add(lca.phylum)
else:
c.phylum_unmapped += 1
if lca.phylum_plus != "NA":
nreads_phylum_plus += 1
level_counts["phylum+"].add(lca.phylum_plus)
else:
c.phylum_plus_unmapped += 1
if lca._class != "NA":
nreads_class += 1
level_counts["class"].add(lca._class)
else:
c.class_unmapped += 1
if lca._class_plus != "NA":
nreads_class_plus += 1
level_counts["class+"].add(lca._class_plus)
else:
c.class_plus_unmapped += 1
if lca.order != "NA":
nreads_order += 1
level_counts["order"].add(lca.order)
else:
c.order_unmapped += 1
if lca.order_plus != "NA":
nreads_order_plus += 1
level_counts["order+"].add(lca.order_plus)
else:
c.order_plus_unmapped += 1
if lca.family != "NA":
nreads_family += 1
level_counts["family"].add(lca.family)
else:
c.family_unmapped += 1
if lca.family != "NA":
nreads_family_plus == 1
level_counts["family+"].add(lca.family_plus)
else:
c.family_plus_unmapped += 1
if lca.genus != "NA":
nreads_genus += 1
level_counts["genus"].add(lca.genus)
else:
c.genus_unmapped += 1
if lca.genus_plus != "NA":
nreads_genus_plus == 1
level_counts["genus+"].add(lca.genus_plus)
else:
c.genus_plus_unmapped += 1
if lca.species != "NA":
nreads_species += 1
level_counts["species"].add(lca.species)
else:
c.species_unmapped += 1
if lca.species_plus != "NA":
nreads_species_plus += 1
level_counts["species+"].add(lca.species_plus)
else:
c.species_plus_unmapped += 1
if lca.subspecies != "NA":
nreads_subspecies += 1
level_counts["subspecies"].add(lca.subspecies)
else:
c.subspecies_unmapped += 1
if lca.subspecies_plus != "NA":
nreads_subspecies_plus += 1
level_counts["subspecies+"].add(lca.subspecies_plus)
else:
c.subspecies_plus_unmapped += 1
options.stdout.write("\t".join(["nkingdom", "nkingdom+", "nphylum", "nphylum+", "nclass", "nclass+", "norder", "norder+", "nfamily", "nfamily+", "ngenus", "ngenus+", "nspecies", "nspecies+", "nsubspecies", "nsubspecies+", "nseqkingdom",
"nseqkingdom+", "nseqphylum", "nseqphylum+", "nseqclass", "nseqclass+", "nseqorder", "nseqorder+", "nseqfamily", "nseqfamily+", "nseqgenus", "nseqgenus+", "nseqspecies", "nseqspecies+", "nseqsubspecies", "nseqsubspecies+"]) + "\n")
options.stdout.write("\t".join(map(str, [len(level_counts["kingdom"]), len(level_counts["kingdom+"]), len(level_counts["phylum"]), len(level_counts["phylum+"]), len(level_counts["class"]), len(level_counts["class+"]), len(level_counts["order"]), len(level_counts["order+"]), len(level_counts["family"]), len(level_counts["family+"]), len(level_counts["genus"]), len(level_counts["genus+"]), len(
level_counts["species"]), len(level_counts["species+"]), len(level_counts["subspecies"]), len(level_counts["subspecies+"]), nreads_kingdom, nreads_phylum, nreads_phylum_plus, nreads_class, nreads_class_plus, nreads_order, nreads_order_plus, nreads_family, nreads_family_plus, nreads_genus, nreads_genus_plus, nreads_species, nreads_species_plus, nreads_subspecies, nreads_subspecies_plus])) + "\n")
elif options.summarise == "taxa-counts":
unmapped = collections.defaultdict(int)
total = 0
taxa_counts = {"kingdom": collections.defaultdict(int), "kingdom+": collections.defaultdict(int), "phylum": collections.defaultdict(int), "phylum+": collections.defaultdict(int), "class": collections.defaultdict(int), "class+": collections.defaultdict(int), "order": collections.defaultdict(int), "order+": collections.defaultdict(
int), "family": collections.defaultdict(int), "family+": collections.defaultdict(int), "genus": collections.defaultdict(int), "genus+": collections.defaultdict(int), "species": collections.defaultdict(int), "species+": collections.defaultdict(int), "subspecies": collections.defaultdict(int), "subspecies+": collections.defaultdict(int)}
c = E.Counter()
for lca in LCA.iterate(options.stdin):
total += 1
if lca.kingdom != "NA":
taxa_counts["kingdom"][lca.kingdom] += 1
else:
c.kingdom_unmapped += 1
unmapped["kingdom"] += 1
if lca.kingdom_plus != "NA":
taxa_counts["kingdom+"][lca.kingdom_plus] += 1
else:
c.kingdom_plus_unmapped += 1
unmapped["kingdom+"] += 1
if lca.phylum != "NA":
taxa_counts["phylum"][lca.phylum] += 1
else:
c.phylum_unmapped += 1
unmapped["phylum"] += 1
if lca.phylum_plus != "NA":
taxa_counts["phylum+"][lca.phylum_plus] += 1
else:
c.phylum_plus_unmapped += 1
unmapped["phylum+"] += 1
if lca._class != "NA":
taxa_counts["class"][lca._class] += 1
else:
c.class_unmapped += 1
unmapped["class"] += 1
if lca._class_plus != "NA":
taxa_counts["class+"][lca._class_plus] += 1
else:
c.class_plus_unmapped += 1
unmapped["class+"] += 1
if lca.order != "NA":
taxa_counts["order"][lca.order] += 1
else:
c.order_unmapped += 1
unmapped["order"] += 1
if lca.order_plus != "NA":
taxa_counts["order+"][lca.order_plus] += 1
else:
c.order_plus_unmapped += 1
unmapped["order+"] += 1
if lca.family != "NA":
taxa_counts["family"][lca.family] += 1
else:
c.family_unmapped += 1
unmapped["family"] += 1
if lca.family_plus != "NA":
taxa_counts["family+"][lca.family_plus] += 1
else:
c.family_plus_unmapped += 1
unmapped["family+"] += 1
if lca.genus != "NA":
taxa_counts["genus"][lca.genus] += 1
else:
c.genus_unmapped += 1
unmapped["genus"] += 1
if lca.genus_plus != "NA":
taxa_counts["genus+"][lca.genus_plus] += 1
else:
c.genus_plus_unmapped += 1
unmapped["genus+"] += 1
if lca.species != "NA":
taxa_counts["species"][lca.species] += 1
else:
c.species_unmapped += 1
unmapped["species"] += 1
if lca.species_plus != "NA":
taxa_counts["species+"][lca.species_plus] += 1
else:
c.species_plus_unmapped += 1
unmapped["species+"] += 1
if lca.subspecies != "NA":
taxa_counts["subspecies"][lca.subspecies] += 1
else:
c.subspecies_unmapped += 1
unmapped["subspecies"] += 1
if lca.subspecies_plus != "NA":
taxa_counts["subspecies+"][lca.subspecies_plus] += 1
else:
c.subspecies_plus_unmapped += 1
unmapped["subspecies+"] += 1
options.stdout.write("level\ttaxa\tcount\tproportion\n")
for level, taxa_count in taxa_counts.iteritems():
total_level = total - unmapped[level]
for taxa, count in taxa_count.iteritems():
options.stdout.write(
"\t".join([level, taxa, str(count), str(float(count) / total_level)]) + "\n")
E.info(c)
elif options.summarise == "individual":
# each read is output with its respective
# taxon assignments
options.stdout.write("\t".join(["id", "kingdom", "kingdom+", "phylum", "phylum+", "class", "class+", "order",
"order+", "family", "family+", "genus", "genus+", "species", "species+", "subspecies", "subspecies+"]) + "\n")
for lca in LCA.iterate(options.stdin):
options.stdout.write("\t".join([lca.identifier, lca.kingdom, lca.kingdom_plus, lca.phylum, lca.phylum_plus, lca._class, lca._class_plus, lca.order,
lca.order_plus, lca.family, lca.family_plus, lca.genus, lca.genus_plus, lca.species, lca.species_plus, lca.subspecies, lca.subspecies_plus]) + "\n")
# write footer and output benchmark information.
E.Stop()
