def main():
args=parse_arguments(sys)
try:
file_handle_write=open(args.output,"wt")
except EnvironmentError:
sys.exit("Error: Unable to open output file: " + args.output)
try:
file_handle_read=open(args.input,"rt")
except EnvironmentError:
sys.exit("Error: Unable to read input file: " + args.input)
# write the header to the new file
file_handle_write.write(file_handle_read.readline())
# trim the taxonomy
for line in file_handle_read:
# ignore lines that are comments
if line.startswith("#"):
file_handle_write.write(line)
else:
data=line.rstrip().split("\t")
if args.taxonomy_column is None:
# try to figure out which column has the taxonomy data
try:
args.taxonomy_column=[index for index, value in enumerate(data) if "k__" in value][0]
except IndexError:
sys.exit("Error unable to find the taxonomy column. Please provide it with the option --taxonomy-column <0>.")
data[args.taxonomy_column]=utilities.taxonomy_trim([data[args.taxonomy_column]])[0]
file_handle_write.write("\t".join(data)+"\n")
file_handle_read.close()
file_handle_write.close()
def test_taxonomy_trim(self):
""" Test the taxonomy trim function """
taxa = [
"k__k3;p__p3;c__c2;o__o3;f__;g__;s__",
"k__k3;p__p3;c__c2;o__o3;f__f1;g__g1;s__",
"k__k3;p__p3;c__c2;o__o3;f__f1;g__g1;s__s1",
"k__k3;p__p3;c__c2;o__o3;f__f1;g__;s__"
]
expected_taxa = [
"o__o3.f__.g__.s__", "g__g1.s__", "g__g1.s__s1", "f__f1.g__.s__"
]
self.assertEqual(utilities.taxonomy_trim(taxa), expected_taxa)
#' ## Terminal Taxa
#+ echo=False
# plot the relative abundance of the top terminal taxa
# get the terminal taxa
terminal_taxa_relab, terminal_data_relab = utilities.terminal_taxa(
taxonomy, relab_data)
# get the top rows of terminal taxa
top_terminal_taxa, top_terminal_data = utilities.top_rows(terminal_taxa_relab,
terminal_data_relab,
max_taxa,
function="average")
# reduce the taxa names to just the most specific identifier
shorted_names = utilities.taxonomy_trim(top_terminal_taxa)
# sort the data with the samples with the top terminal taxa first
sorted_samples_terminal, sorted_data_terminal = utilities.sort_data(
top_terminal_data[0], samples)
transpose_top_terminal_data = numpy.transpose(top_terminal_data)
sorted_top_terminal_data = numpy.transpose([
transpose_top_terminal_data[samples.index(sample)]
for sample in sorted_samples_terminal
])
# add the remaining terminal taxa as "other" to the data
shorted_names_plus_other, sorted_top_terminal_data_plus_other = visualizations.fill_taxonomy_other(
shorted_names, sorted_top_terminal_data)
document.plot_stacked_barchart(sorted_top_terminal_data_plus_other,
def main():
args = parse_arguments(sys)
try:
file_handle_write = open(args.output, "wt")
except EnvironmentError:
sys.exit("Error: Unable to open output file: " + args.output)
try:
if args.input.endswith(".gz"):
file_handle_read = gzip.open(args.input, "rt")
else:
file_handle_read = open(args.input, "rt")
except EnvironmentError:
sys.exit("Error: Unable to read input file: " + args.input)
# write the header to the new file
header = file_handle_read.readline().rstrip().split("\t")
# ignore comment if present
if header[0].startswith(BIOM_COMMENT):
header = file_handle_read.readline().rstrip().split("\t")
# trim the taxonomy and sum species
taxonomy_data = {}
for line in file_handle_read:
# ignore lines that are comments
if line.startswith("#"):
file_handle_write.write(line)
else:
data = line.rstrip().split("\t")
if args.taxonomy_column is None:
# try to figure out which column has the taxonomy data
try:
args.taxonomy_column = [
index for index, value in enumerate(data)
if "k__" in value
][0]
except IndexError:
sys.exit(
"Error unable to find the taxonomy column. Please provide it with the option --taxonomy-column <0>."
)
if args.end_taxonomy_column is None:
args.end_taxonomy_column = args.taxonomy_column
new_taxonomy = utilities.taxonomy_trim(
[data[args.taxonomy_column]])[0]
data.pop(args.taxonomy_column)
if new_taxonomy in taxonomy_data:
data = [data[0]] + [
str(float(a) + float(b))
for a, b in zip(taxonomy_data[new_taxonomy][1:], data[1:])
]
taxonomy_data[new_taxonomy] = data
# write the header
old_taxon = header.pop(args.taxonomy_column)
header[args.end_taxonomy_column] = old_taxon
file_handle_write.write("\t".join(header) + "\n")
# write the new data
for taxon, data in taxonomy_data.items():
data[args.end_taxonomy_column] = taxon
file_handle_write.write("\t".join(data) + "\n")
file_handle_read.close()
file_handle_write.close()