def test_plot_rank_abundance_graphs_dense(self):
"""plot_rank_abundance_graphs works with any number of samples (DenseOTUTable)"""
self.otu_table = parse_biom_table_str(otu_table_dense)
self.dir = get_tmp_filename(tmp_dir=self.tmp_dir,
prefix="test_plot_rank_abundance",
suffix="/")
create_dir(self.dir)
self._dirs_to_remove.append(self.dir)
#test empty sample name
self.assertRaises(ValueError, plot_rank_abundance_graphs, '',
self.otu_table, self.dir)
#test invalid sample name
self.assertRaises(ValueError, plot_rank_abundance_graphs,
'Invalid_sample_name',
self.otu_table, self.dir)
#test with two samples
file_type="pdf"
plot_rank_abundance_graphs('S3,S5', self.otu_table, self.dir,
file_type=file_type)
tmp_file = abspath(self.dir+"rank_abundance_cols_0_2."+file_type)
self.assertTrue(exists(tmp_file))
self.files_to_remove.append(tmp_file)
# test with all samples
plot_rank_abundance_graphs('*', self.otu_table, self.dir,
file_type=file_type)
tmp_file = abspath(self.dir+"rank_abundance_cols_0_1_2."+file_type)
self.files_to_remove.append(tmp_file)
self.assertTrue(exists(tmp_file))
def test_plot_rank_abundance_graphs_dense(self):
"""plot_rank_abundance_graphs works with any number of samples (DenseOTUTable)"""
self.otu_table = parse_biom_table_str(otu_table_dense)
self.dir = get_tmp_filename(tmp_dir=self.tmp_dir,
prefix="test_plot_rank_abundance",
suffix="/")
create_dir(self.dir)
self._dirs_to_remove.append(self.dir)
tmp_fname = get_tmp_filename(tmp_dir=self.dir)
#test empty sample name
self.assertRaises(ValueError, plot_rank_abundance_graphs, tmp_fname,'',
self.otu_table)
#test invalid sample name
self.assertRaises(ValueError, plot_rank_abundance_graphs, tmp_fname,
'Invalid_sample_name',
self.otu_table)
#test with two samples
file_type="pdf"
tmp_file = abspath(self.dir+"rank_abundance_cols_0_2."+file_type)
plot_rank_abundance_graphs(tmp_file, 'S3,S5', self.otu_table,
file_type=file_type)
self.assertTrue(exists(tmp_file))
self.files_to_remove.append(tmp_file)
# test with all samples
tmp_file = abspath(self.dir+"rank_abundance_cols_0_1_2."+file_type)
plot_rank_abundance_graphs(tmp_file,'*', self.otu_table,file_type=file_type)
self.files_to_remove.append(tmp_file)
self.assertTrue(exists(tmp_file))
def test_plot_rank_abundance_graphs(self):
"""plot_rank_abundance_graphs works with any number of samples"""
self.otu_table = otu_table_fake.split("\n")
self.dir = get_tmp_filename(tmp_dir=self.tmp_dir, prefix="test_plot_rank_abundance", suffix="/")
create_dir(self.dir)
self._dirs_to_remove.append(self.dir)
# test empty sample name
self.assertRaises(ValueError, plot_rank_abundance_graphs, "", iter(self.otu_table), self.dir)
# test invalid sample name
self.assertRaises(ValueError, plot_rank_abundance_graphs, "Invalid_sample_name", iter(self.otu_table), self.dir)
# test with two samples
file_type = "pdf"
plot_rank_abundance_graphs("S3,S5", iter(self.otu_table), self.dir, file_type=file_type)
tmp_file = abspath(self.dir + "rank_abundance_cols_0_2." + file_type)
self.assertTrue(exists(tmp_file))
self.files_to_remove.append(tmp_file)
# test with all samples
plot_rank_abundance_graphs("*", iter(self.otu_table), self.dir, file_type=file_type)
tmp_file = abspath(self.dir + "rank_abundance_cols_0_1_2." + file_type)
self.files_to_remove.append(tmp_file)
self.assertTrue(exists(tmp_file))
def test_plot_rank_abundance_graphs_filetype(self):
"""plot_rank_abundance_graphs works with all filetypes"""
self.otu_table = otu_table_fake.split("\n")
self.dir = get_tmp_filename(tmp_dir=self.tmp_dir, prefix="test_plot_rank_abundance", suffix="/")
create_dir(self.dir)
self._dirs_to_remove.append(self.dir)
# test all supported filetypes
for file_type in ["pdf", "svg", "png", "eps"]:
plot_rank_abundance_graphs("S3", iter(self.otu_table), self.dir, file_type=file_type)
tmp_file = abspath(self.dir + "rank_abundance_cols_0." + file_type)
self.files_to_remove.append(tmp_file)
self.assertTrue(exists(tmp_file))
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
otu_table_fp = opts.otu_table_fp
sample_name = opts.sample_name
log_fn = opts.result_fp + "_log.txt"
log_fh = open(log_fn, 'w')
log_fh.write("OTU table file: %s\n" % otu_table_fp)
log_fh.write("sample names: %s\n" % sample_name)
otu_table = load_table(opts.otu_table_fp)
plot_rank_abundance_graphs(opts.result_fp, opts.sample_name, otu_table,
opts.file_type, opts.absolute_counts,
opts.x_linear_scale, opts.y_linear_scale,
opts.no_legend, log_fh)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
otu_table_fp = opts.otu_table_fp
sample_name = opts.sample_name
log_fn = opts.result_fp + "_log.txt"
log_fh = open(log_fn, 'w')
log_fh.write("OTU table file: %s\n" % otu_table_fp)
log_fh.write("sample names: %s\n" % sample_name)
otu_table = load_table(opts.otu_table_fp)
plot_rank_abundance_graphs(opts.result_fp, opts.sample_name, otu_table,
opts.file_type,
opts.absolute_counts, opts.x_linear_scale,
opts.y_linear_scale, opts.no_legend, log_fh)
def test_plot_rank_abundance_graphs_filetype(self):
"""plot_rank_abundance_graphs works with all filetypes"""
self.otu_table = parse_biom_table_str(otu_table_sparse)
self.dir = get_tmp_filename(tmp_dir=self.tmp_dir,
prefix="test_plot_rank_abundance",
suffix="/")
create_dir(self.dir)
self._dirs_to_remove.append(self.dir)
#test all supported filetypes
for file_type in ['pdf','svg','png','eps']:
plot_rank_abundance_graphs('S3', self.otu_table, self.dir,
file_type=file_type)
tmp_file = abspath(self.dir+"rank_abundance_cols_0."+file_type)
self.files_to_remove.append(tmp_file)
self.assertTrue(exists(tmp_file))
def test_plot_rank_abundance_graphs_filetype(self):
"""plot_rank_abundance_graphs works with all filetypes"""
self.otu_table = parse_biom_table_str(otu_table_sparse)
self.dir = get_tmp_filename(tmp_dir=self.tmp_dir,
prefix="test_plot_rank_abundance",
suffix="/")
create_dir(self.dir)
self._dirs_to_remove.append(self.dir)
#test all supported filetypes
for file_type in ['pdf','svg','png','eps']:
tmp_file = abspath(self.dir+"rank_abundance_cols_0."+file_type)
plot_rank_abundance_graphs(tmp_file,'S3', self.otu_table, file_type=file_type)
self.files_to_remove.append(tmp_file)
self.assertTrue(exists(tmp_file))
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
output_dir = opts.output_dir
otu_table_fp = opts.otu_table_fp
sample_name = opts.sample_name
create_dir(output_dir)
if opts.verbose:
log_fh = open(output_dir+"/plot_rank_abundance_log.txt",'w')
log_fh.write("OTU table file: %s\n"% otu_table_fp)
log_fh.write("sample names: %s\n" % sample_name)
else:
log_fh=None
otu_table = parse_biom_table(open(opts.otu_table_fp,"U"))
plot_rank_abundance_graphs(opts.sample_name, otu_table,
output_dir, opts.file_type,
opts.absolute_counts, opts.x_linear_scale,
opts.y_linear_scale, opts.no_legend, log_fh)
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
#set up and create the outpurt dir
if opts.output_dir:
output_dir = opts.output_dir
else:
output_dir = get_tmp_filename(tmp_dir='./', prefix='rank_abundance_', suffix='')
create_dir(output_dir, fail_on_exist=True)
if opts.verbose:
log_fh = open(output_dir+"/plot_rank_abundance_log.txt",'w')
log_fh.write("OTU table file: %s\n"% opts.otu_table_fp)
log_fh.write("sample names: %s\n" % opts.sample_name)
else:
log_fh=None
plot_rank_abundance_graphs(opts.sample_name, open(opts.otu_table_fp,"U"),
output_dir, opts.file_type,
opts.absolute_counts, opts.x_linear_scale,
opts.y_linear_scale, opts.no_legend, log_fh)
def test_plot_rank_abundance_graphs(self):
"""plot_rank_abundance_graphs works with any number of samples (Table)"""
self.otu_table = parse_biom_table(otu_table_sparse)
self.dir = mkdtemp(dir=self.tmp_dir,
prefix="test_plot_rank_abundance",
suffix="/")
self._dirs_to_remove.append(self.dir)
fd, tmp_fname = mkstemp(dir=self.dir)
close(fd)
# test empty sample name
self.assertRaises(
ValueError, plot_rank_abundance_graphs, tmp_fname, '',
self.otu_table)
# test invalid sample name
self.assertRaises(ValueError, plot_rank_abundance_graphs, tmp_fname,
'Invalid_sample_name',
self.otu_table)
# test with two samples
file_type = "pdf"
tmp_file = abspath(self.dir + "rank_abundance_cols_0_2." + file_type)
plot_rank_abundance_graphs(tmp_file, 'S3,S5', self.otu_table,
file_type=file_type)
self.assertTrue(exists(tmp_file))
self.files_to_remove.append(tmp_file)
# test with all samples
tmp_file = abspath(self.dir + "rank_abundance_cols_0_1_2." + file_type)
plot_rank_abundance_graphs(tmp_file, '*', self.otu_table,
file_type=file_type)
self.files_to_remove.append(tmp_file)
self.assertTrue(exists(tmp_file))