def test_write_combined_fasta(self):
""" Properly writes combined fasta data """
mapping_data = {
'%s' % basename(self.fasta1_fp): 'Sample1',
'%s' % basename(self.fasta2_fp): 'Sample2',
'%s' % basename(self.fasta3_fp): 'Sample3'
}
fasta_fps = [self.fasta2_fp, self.fasta3_fp, self.fasta1_fp]
write_combined_fasta(mapping_data,
fasta_fps,
self.output_dir,
counter=100)
output_fp = open(join(self.output_dir, "combined_seqs.fna"), "U")
output_lines = [line.strip() for line in output_fp]
expected_output_lines = [
'>Sample2_100 label3 ZZZ', 'AACGYAACGAGA', '>Sample2_101 label4',
'ACAGAGAGAGGGGAGA', '>Sample3_102 label5 ;LKJ', 'ACAGGGATTTTTAT',
'>Sample1_103 label1 XXX', 'ACAGATTACGA',
'>Sample1_104 label2 YYY', 'ACATAAAATAGCCGGAG'
]
self.assertEqual(output_lines, expected_output_lines)
def test_write_combined_fasta(self):
""" Properly writes combined fasta data """
mapping_data = {
"%s" % basename(self.fasta1_fp): "Sample1",
"%s" % basename(self.fasta2_fp): "Sample2",
"%s" % basename(self.fasta3_fp): "Sample3",
}
fasta_fps = [self.fasta2_fp, self.fasta3_fp, self.fasta1_fp]
write_combined_fasta(mapping_data, fasta_fps, self.output_dir, counter=100)
output_fp = open(join(self.output_dir, "combined_seqs.fna"), "U")
output_lines = [line.strip() for line in output_fp]
expected_output_lines = [
">Sample2_100 label3 ZZZ",
"AACGYAACGAGA",
">Sample2_101 label4",
"ACAGAGAGAGGGGAGA",
">Sample3_102 label5 ;LKJ",
"ACAGGGATTTTTAT",
">Sample1_103 label1 XXX",
"ACAGATTACGA",
">Sample1_104 label2 YYY",
"ACATAAAATAGCCGGAG",
]
self.assertEqual(output_lines, expected_output_lines)
def test_write_combined_fasta(self):
""" Properly writes combined fasta data """
mapping_data = {'%s' % basename(self.fasta1_fp): 'Sample1',
'%s' % basename(self.fasta2_fp): 'Sample2',
'%s' % basename(self.fasta3_fp): 'Sample3'
}
fasta_fps = [self.fasta2_fp, self.fasta3_fp, self.fasta1_fp]
write_combined_fasta(mapping_data, fasta_fps, self.output_dir,
counter=100)
output_fp = open(join(self.output_dir, "combined_seqs.fna"), "U")
output_lines = [line.strip() for line in output_fp]
expected_output_lines = ['>Sample2_100 label3 ZZZ', 'AACGYAACGAGA',
'>Sample2_101 label4', 'ACAGAGAGAGGGGAGA',
'>Sample3_102 label5 ;LKJ', 'ACAGGGATTTTTAT',
'>Sample1_103 label1 XXX', 'ACAGATTACGA',
'>Sample1_104 label2 YYY', 'ACATAAAATAGCCGGAG'
]
self.assertEqual(output_lines, expected_output_lines)