def test_format_tep_file_lines(self):
""" format_tep_file_lines: this converts files into tep lines """
# set variables
prefs_dict1 = {'sample_coloring': {'TEST1': {'column': 'TEST1',
'colors': (('red', (0, 100, 100)), ('blue', (240, 100, 100)))}}}
test_biom2 = parse_biom_table(biom2)
# test with prefs file
exp1 = ['>>tre\n', "['(tax1:0.00000043418318065054,((tax2:0.01932550067944402081,tax3:0.08910446960529855298):0.00000043418318065054,tax4:0.17394765077611337722):0.00000043418318065054,tax5:0.00000043418318065054):0.0;']", '\n', '>>otm\n#OTU ID\tOTU Metadata\n', u'tax1\tk__Bacteria;p__Proteobacteria;', '\n', u'tax2\tk__Bacteria;p__Cyanobacteria;', '\n', '>>osm\n', '# Constructed from biom file\n#OTU ID\tsam1\tsam2\tConsensus Lineage\ntax1\t7.0\t4.0\tk__Bacteria;p__Proteobacteria\ntax2\t1.0\t2.0\tk__Bacteria;p__Cyanobacteria', '\n>>sam\n', "['#SampleID\\tcol1\\tcol0\\tDescription', 'sam1\\tv1_3\\tv0_3\\td1', 'sam2\\taval\\tanother\\td2']", '\n>>pre\n', '0,100,100,\n', '240,100,100,\n', '>defaultTEST1:TEST1\n']
obs1 = format_tep_file_lines(test_biom2,
StringIO(example_mapping_file2.split('\n')),
StringIO(example_tree.split('\n')),
prefs_dict1)
self.assertEqual(obs1,exp1)
# test without prefs file
exp2 = ['>>tre\n', "['(tax1:0.00000043418318065054,((tax2:0.01932550067944402081,tax3:0.08910446960529855298):0.00000043418318065054,tax4:0.17394765077611337722):0.00000043418318065054,tax5:0.00000043418318065054):0.0;']", '\n', '>>otm\n#OTU ID\tOTU Metadata\n', u'tax1\tk__Bacteria;p__Proteobacteria;', '\n', u'tax2\tk__Bacteria;p__Cyanobacteria;', '\n', '>>osm\n', '# Constructed from biom file\n#OTU ID\tsam1\tsam2\tConsensus Lineage\ntax1\t7.0\t4.0\tk__Bacteria;p__Proteobacteria\ntax2\t1.0\t2.0\tk__Bacteria;p__Cyanobacteria', '\n>>sam\n', "['#SampleID\\tcol1\\tcol0\\tDescription', 'sam1\\tv1_3\\tv0_3\\td1', 'sam2\\taval\\tanother\\td2']"]
obs2 = format_tep_file_lines(test_biom2,
StringIO(example_mapping_file2.split('\n')),
StringIO(example_tree.split('\n')),
{})
self.assertEqual(obs2,exp2)
def test_format_tep_file_lines(self):
""" format_tep_file_lines: this converts files into tep lines """
# set variables
prefs_dict1 = {'sample_coloring': {'TEST1': {'column': 'TEST1',
'colors': (('red', (0, 100, 100)), ('blue', (240, 100, 100)))}}}
test_biom2 = parse_biom_table(biom2)
# test with prefs file
exp1 = [
'>>tre\n',
"['(tax1:0.00000043418318065054,((tax2:0.01932550067944402081,tax3:0.08910446960529855298):0.00000043418318065054,tax4:0.17394765077611337722):0.00000043418318065054,tax5:0.00000043418318065054):0.0;']",
'\n',
'>>otm\n#OTU ID\tOTU Metadata\n',
u'tax1\tk__Bacteria;p__Proteobacteria;',
'\n',
u'tax2\tk__Bacteria;p__Cyanobacteria;',
'\n',
'>>osm\n',
'# Constructed from biom file\n#OTU ID\tsam1\tsam2\tConsensus Lineage\ntax1\t7.0\t4.0\tk__Bacteria;p__Proteobacteria\ntax2\t1.0\t2.0\tk__Bacteria;p__Cyanobacteria',
'\n>>sam\n',
"['#SampleID\\tcol1\\tcol0\\tDescription', 'sam1\\tv1_3\\tv0_3\\td1', 'sam2\\taval\\tanother\\td2']",
'\n>>pre\n',
'0,100,100,\n',
'240,100,100,\n',
'>defaultTEST1:TEST1\n']
obs1 = format_tep_file_lines(test_biom2,
StringIO(
example_mapping_file2.split('\n')),
StringIO(example_tree.split('\n')),
prefs_dict1)
self.assertEqual(obs1, exp1)
# test without prefs file
exp2 = [
'>>tre\n',
"['(tax1:0.00000043418318065054,((tax2:0.01932550067944402081,tax3:0.08910446960529855298):0.00000043418318065054,tax4:0.17394765077611337722):0.00000043418318065054,tax5:0.00000043418318065054):0.0;']",
'\n',
'>>otm\n#OTU ID\tOTU Metadata\n',
u'tax1\tk__Bacteria;p__Proteobacteria;',
'\n',
u'tax2\tk__Bacteria;p__Cyanobacteria;',
'\n',
'>>osm\n',
'# Constructed from biom file\n#OTU ID\tsam1\tsam2\tConsensus Lineage\ntax1\t7.0\t4.0\tk__Bacteria;p__Proteobacteria\ntax2\t1.0\t2.0\tk__Bacteria;p__Cyanobacteria',
'\n>>sam\n',
"['#SampleID\\tcol1\\tcol0\\tDescription', 'sam1\\tv1_3\\tv0_3\\td1', 'sam2\\taval\\tanother\\td2']"]
obs2 = format_tep_file_lines(test_biom2,
StringIO(
example_mapping_file2.split('\n')),
StringIO(example_tree.split('\n')),
{})
self.assertEqual(obs2, exp2)
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
# get command line arguments
otu_table_fp = opts.otu_table_fp
mapping_fp = opts.mapping_fp
tree_fp = opts.tree_fp
output_dir = opts.output_dir
output_basename = splitext(split(otu_table_fp)[1])[0]
web_flag = opts.web_flag
url = opts.url
# create a generic output folder if not present
if not output_dir:
output_dir = 'make_tep_output/'
create_dir(output_dir)
# open files for parsing
otu_table_data = parse_biom_table(open(otu_table_fp, 'U'))
mapping_lines = open(mapping_fp, 'U')
tree_lines = open(tree_fp, 'U')
prefs_dict = {}
if opts.prefs_file_fp:
prefs_fp = opts.prefs_file_fp
# I don't like this eval statement
prefs_dict = eval(open(prefs_fp, 'U').read())
# get the tep file lines
lines = format_tep_file_lines(otu_table_data, mapping_lines, tree_lines,
prefs_dict)
# write tep file lines if url path not given
tep_fp = '%s/%s.tep' % (output_dir, output_basename)
if not url:
# write tep file
tepfile = open(tep_fp, 'w')
tepfile.writelines(lines)
tepfile.close()
# get the jnlp file lines
lines = format_jnlp_file_lines(web_flag, url, tep_fp)
# write jnlp file
jnlp_fp = '%s/%s.jnlp' % (output_dir, output_basename)
jnlpfile = open(jnlp_fp, 'w')
jnlpfile.writelines(lines)
jnlpfile.close()
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
# get command line arguments
otu_table_fp = opts.otu_table_fp
mapping_fp = opts.mapping_fp
tree_fp = opts.tree_fp
output_dir = opts.output_dir
output_basename = splitext(split(otu_table_fp)[1])[0]
web_flag = opts.web_flag
url = opts.url
# create a generic output folder if not present
if not output_dir:
output_dir = 'make_tep_output/'
create_dir(output_dir)
# open files for parsing
otu_table_data = parse_biom_table(open(otu_table_fp, 'U'))
mapping_lines = open(mapping_fp, 'U')
tree_lines = open(tree_fp, 'U')
prefs_dict={}
if opts.prefs_file_fp:
prefs_fp = opts.prefs_file_fp
# I don't like this eval statement
prefs_dict = eval(open(prefs_fp,'U').read())
# get the tep file lines
lines = format_tep_file_lines(otu_table_data, mapping_lines, tree_lines,
prefs_dict)
# write tep file lines if url path not given
tep_fp = '%s/%s.tep' % (output_dir,output_basename)
if not url:
# write tep file
tepfile = open(tep_fp, 'w')
tepfile.writelines(lines)
tepfile.close()
# get the jnlp file lines
lines = format_jnlp_file_lines(web_flag, url, tep_fp)
# write jnlp file
jnlp_fp = '%s/%s.jnlp' % (output_dir,output_basename)
jnlpfile = open(jnlp_fp, 'w')
jnlpfile.writelines(lines)
jnlpfile.close()
