def test_handle_no_reads_map_to_reverse_strand(self):
"""Fastqstrand handles case when no reads map to reverse strand
"""
self._write_file(
"""#fastq_strand version: 0.0.3 #Aligner: STAR #Reads in subset: 6
#Genome 1st forward 2nd reverse
human 100.00 0.00
""")
fastq_strand = Fastqstrand(self.fastq_strand_txt)
self.assertEqual(fastq_strand.version, '0.0.3')
self.assertEqual(fastq_strand.txt, self.fastq_strand_txt)
self.assertEqual(fastq_strand.genomes, [
'human',
])
self.assertEqual(fastq_strand.stats['human'].forward, 100.00)
self.assertEqual(fastq_strand.stats['human'].reverse, 0.00)
self.assertEqual(fastq_strand.stats['human'].ratio, float("+inf"))
self.assertEqual(fastq_strand.stats['human'].strandedness, "forward")
def test_handle_fastq_strand_0_0_1(self):
"""Fastqstrand handles output from version 0.0.1
"""
self._write_file(
"""#fastq_strand version: 0.0.1 #Aligner: STAR #Reads in subset: 3
#Genome 1st forward 2nd reverse
hg38 13.13 93.21
mm10 15.02 91.18
""")
fastq_strand = Fastqstrand(self.fastq_strand_txt)
self.assertEqual(fastq_strand.version, '0.0.1')
self.assertEqual(fastq_strand.txt, self.fastq_strand_txt)
self.assertEqual(fastq_strand.genomes, ['hg38', 'mm10'])
self.assertEqual(fastq_strand.stats['hg38'].forward, 13.13)
self.assertEqual(fastq_strand.stats['hg38'].reverse, 93.21)
self.assertEqual("%.4f" % fastq_strand.stats['hg38'].ratio,
"%.4f" % 0.140864714)
self.assertEqual(fastq_strand.stats['hg38'].strandedness, "reverse")
self.assertEqual(fastq_strand.stats['mm10'].forward, 15.02)
self.assertEqual(fastq_strand.stats['mm10'].reverse, 91.18)
self.assertEqual("%.4f" % fastq_strand.stats['mm10'].ratio,
"%.4f" % 0.164729107)
self.assertEqual(fastq_strand.stats['mm10'].strandedness, "reverse")