def test_add_qiime_labels_valid_data(self):
""" Tests overall script functionality """
# With valid data should not raise any errors
mapping_data = [
'#SampleID BarcodeSequence LinkerPrimerSequence InputFileNames Description',
'Sample1 AAAA ACTG %s S1' % basename(self.fasta1_fp),
'Sample2 TTTT ACTG %s S2' % basename(self.fasta2_fp),
'Sample3 CCCC ACTG %s S3' % basename(self.fasta3_fp)
]
filename_column = "InputFileNames"
add_qiime_labels(mapping_data, self.input_dir, filename_column,
self.output_dir)
output_fp = open(join(self.output_dir, "combined_seqs.fna"), "U")
output_lines = [line.strip() for line in output_fp]
expected_output_lines = [
'>Sample1_0 label1 XXX', 'ACAGATTACGA', '>Sample1_1 label2 YYY',
'ACATAAAATAGCCGGAG', '>Sample2_2 label3 ZZZ', 'AACGYAACGAGA',
'>Sample2_3 label4', 'ACAGAGAGAGGGGAGA', '>Sample3_4 label5 ;LKJ',
'ACAGGGATTTTTAT'
]
self.assertEqual(output_lines, expected_output_lines)
def test_add_qiime_labels_valid_data(self):
""" Tests overall script functionality """
# With valid data should not raise any errors
mapping_data = [
'#SampleID BarcodeSequence LinkerPrimerSequence InputFileNames Description',
'Sample1 AAAA ACTG %s S1' % basename(self.fasta1_fp),
'Sample2 TTTT ACTG %s S2' % basename(self.fasta2_fp),
'Sample3 CCCC ACTG %s S3' % basename(self.fasta3_fp)
]
filename_column = "InputFileNames"
add_qiime_labels(mapping_data, self.input_dir, filename_column,
self.output_dir)
output_fp = open(join(self.output_dir, "combined_seqs.fna"), "U")
output_lines = [line.strip() for line in output_fp]
expected_output_lines = ['>Sample1_0 label1 XXX', 'ACAGATTACGA',
'>Sample1_1 label2 YYY', 'ACATAAAATAGCCGGAG', '>Sample2_2 label3 ZZZ',
'AACGYAACGAGA', '>Sample2_3 label4', 'ACAGAGAGAGGGGAGA',
'>Sample3_4 label5 ;LKJ', 'ACAGGGATTTTTAT']
self.assertEqual(output_lines, expected_output_lines)
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
mapping_fp = opts.mapping_fp
fasta_dir = opts.fasta_dir
output_dir = opts.output_dir
count_start = int(opts.count_start)
filename_column = opts.filename_column
# Check input filepaths
try:
test_mapping_f = open(mapping_fp, "U")
except IOError:
raise IOError,("Cannot open mapping filepath "+\
"%s, please check filepath and permissions." % mapping_fp)
if not isdir(fasta_dir):
raise IOError, ("Specified fasta dir " +
"%s, does not exist" % fasta_dir)
# Create output directory, check path/access to mapping file
create_dir(output_dir)
add_qiime_labels(open(mapping_fp, "U"), fasta_dir, filename_column,
output_dir, count_start)
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
mapping_fp = opts.mapping_fp
fasta_dir = opts.fasta_dir
output_dir = opts.output_dir
count_start = int(opts.count_start)
filename_column = opts.filename_column
# Check input filepaths
try:
test_mapping_f = open(mapping_fp, "U")
except IOError:
raise IOError,("Cannot open mapping filepath "+\
"%s, please check filepath and permissions." % mapping_fp)
if not isdir(fasta_dir):
raise IOError,("Specified fasta dir "+
"%s, does not exist" % fasta_dir)
# Create output directory, check path/access to mapping file
create_dir(output_dir)
add_qiime_labels(open(mapping_fp, "U"), fasta_dir, filename_column,
output_dir, count_start)
def test_add_qiime_labels_valid_data(self):
""" Tests overall script functionality """
# With valid data should not raise any errors
mapping_data = ['Sample1\t%s' % basename(self.fasta1_fp),
'Sample2\t%s' % basename(self.fasta2_fp),
'Sample3\t%s' % basename(self.fasta3_fp)
]
add_qiime_labels(mapping_data, self.input_dir,
self.output_dir)
output_fp = open(join(self.output_dir, "combined_seqs.fna"), "U")
output_lines = [line.strip() for line in output_fp]
expected_output_lines = ['>Sample2_0 label3 ZZZ', 'AACGYAACGAGA',
'>Sample2_1 label4', 'ACAGAGAGAGGGGAGA',
'>Sample3_2 label5 ;LKJ', 'ACAGGGATTTTTAT',
'>Sample1_3 label1 XXX', 'ACAGATTACGA',
'>Sample1_4 label2 YYY', 'ACATAAAATAGCCGGAG']
self.assertEqual(output_lines, expected_output_lines)
def test_add_qiime_labels_valid_data(self):
""" Tests overall script functionality """
# With valid data should not raise any errors
mapping_data = [
'Sample1\t%s' % basename(self.fasta1_fp),
'Sample2\t%s' % basename(self.fasta2_fp),
'Sample3\t%s' % basename(self.fasta3_fp)
]
add_qiime_labels(mapping_data, self.input_dir, self.output_dir)
output_fp = open(join(self.output_dir, "combined_seqs.fna"), "U")
output_lines = [line.strip() for line in output_fp]
expected_output_lines = [
'>Sample2_0 label3 ZZZ', 'AACGYAACGAGA', '>Sample2_1 label4',
'ACAGAGAGAGGGGAGA', '>Sample3_2 label5 ;LKJ', 'ACAGGGATTTTTAT',
'>Sample1_3 label1 XXX', 'ACAGATTACGA', '>Sample1_4 label2 YYY',
'ACATAAAATAGCCGGAG'
]
self.assertEqual(output_lines, expected_output_lines)