def test_RecordWithoutAssignedReadPair_CorrectFastqString(self):
read = sam_record_from_sring("HISEQ2500-09:381:HJ2VGBCXX:2:1101:10005:7635 35 R00000042 1619836 99 151M = 1620303 618 CCAGAACAGGCGCGGGAAATGTGCGATACCGCGCGCAAACTGGGCAAGGTGCTGGCCTACGACTTTCACCATCGTTTTGCGCTCGATACGCAACAGCTGCGTGAACAGGTGACCAACGGCGTTTTGGGAGAGATTTACGTTACCACCGCCC DDDDDIIIIIIIIIIIIIIIHIHIIIIIIIIGIIIIIIIIGIIIHHIIIIGIIIIIIIIIIHIIIIIIIIIIIIIIIIIHIICGHIIIIHGIIIIHIIIGIGHIIIIIIIIIHHIIIIGIICHHHHIIHEHIIIIIIIIHHIIIIIHHIII PQ:i:205 SM:i:96 UQ:i:78 MQ:i:96 XQ:i:270 NM:i:2 RG:Z:824f45e8-37f3-4cb9-8a05-63f0b7c9b959")
result = bam2fastq.to_fastq_string(read)
expected = """@HISEQ2500-09:381:HJ2VGBCXX:2:1101:10005:7635 RG:824f45e8-37f3-4cb9-8a05-63f0b7c9b959
CCAGAACAGGCGCGGGAAATGTGCGATACCGCGCGCAAACTGGGCAAGGTGCTGGCCTACGACTTTCACCATCGTTTTGCGCTCGATACGCAACAGCTGCGTGAACAGGTGACCAACGGCGTTTTGGGAGAGATTTACGTTACCACCGCCC
+
DDDDDIIIIIIIIIIIIIIIHIHIIIIIIIIGIIIIIIIIGIIIHHIIIIGIIIIIIIIIIHIIIIIIIIIIIIIIIIIHIICGHIIIIHGIIIIHIIIGIGHIIIIIIIIIHHIIIIGIICHHHHIIHEHIIIIIIIIHHIIIIIHHIII"""
self.assertEqual(result, expected)
def test_RecordWithoutRG_CorrectFastqString(self):
read = sam_record_from_sring("HISEQ2500-09:381:HJ2VGBCXX:2:1101:10005:7635 99 R00000042 1619836 99 151M = 1620303 618 CCAGAACAGGCGCGGGAAATGTGCGATACCGCGCGCAAACTGGGCAAGGTGCTGGCCTACGACTTTCACCATCGTTTTGCGCTCGATACGCAACAGCTGCGTGAACAGGTGACCAACGGCGTTTTGGGAGAGATTTACGTTACCACCGCCC DDDDDIIIIIIIIIIIIIIIHIHIIIIIIIIGIIIIIIIIGIIIHHIIIIGIIIIIIIIIIHIIIIIIIIIIIIIIIIIHIICGHIIIIHGIIIIHIIIGIGHIIIIIIIIIHHIIIIGIICHHHHIIHEHIIIIIIIIHHIIIIIHHIII PQ:i:205 SM:i:96 UQ:i:78 MQ:i:96 XQ:i:270 NM:i:2")
result = bam2fastq.to_fastq_string(read)
expected = """@HISEQ2500-09:381:HJ2VGBCXX:2:1101:10005:7635/1
CCAGAACAGGCGCGGGAAATGTGCGATACCGCGCGCAAACTGGGCAAGGTGCTGGCCTACGACTTTCACCATCGTTTTGCGCTCGATACGCAACAGCTGCGTGAACAGGTGACCAACGGCGTTTTGGGAGAGATTTACGTTACCACCGCCC
+
DDDDDIIIIIIIIIIIIIIIHIHIIIIIIIIGIIIIIIIIGIIIHHIIIIGIIIIIIIIIIHIIIIIIIIIIIIIIIIIHIICGHIIIIHGIIIIHIIIGIGHIIIIIIIIIHHIIIIGIICHHHHIIHEHIIIIIIIIHHIIIIIHHIII"""
self.assertEqual(result, expected)
def test_FullRecord_CorrectFastqString(self):
read = sam_record_from_sring(reads_string.split('\n')[0].strip())
result = bam2fastq.to_fastq_string(read)
expected = """@HISEQ2500-09:381:HJ2VGBCXX:2:1101:10005:7635/1 RG:824f45e8-37f3-4cb9-8a05-63f0b7c9b959
CCAGAACAGGCGCGGGAAATGTGCGATACCGCGCGCAAACTGGGCAAGGTGCTGGCCTACGACTTTCACCATCGTTTTGCGCTCGATACGCAACAGCTGCGTGAACAGGTGACCAACGGCGTTTTGGGAGAGATTTACGTTACCACCGCCC
+
DDDDDIIIIIIIIIIIIIIIHIHIIIIIIIIGIIIIIIIIGIIIHHIIIIGIIIIIIIIIIHIIIIIIIIIIIIIIIIIHIICGHIIIIHGIIIIHIIIGIGHIIIIIIIIIHHIIIIGIICHHHHIIHEHIIIIIIIIHHIIIIIHHIII"""
self.assertEqual(result, expected)
def test_FullReverseRecord_CorrectFastqString(self):
read = sam_record_from_sring(reads_string.split('\n')[4].strip())
result = bam2fastq.to_fastq_string(read)
expected = """@HISEQ2500-09:381:HJ2VGBCXX:2:1101:10005:7635/2 RG:824f45e8-37f3-4cb9-8a05-63f0b7c9b959
ATTGATAAAGGCTTCCATGCTGCGCAAATGGCGGTTGTCGTCTGCCATTTCCCGTTGCATCAGCGTCATTAATTCACCGTTGTTATCGGTGTAGATATGTGCTGGAAACAGCGTCGCACCAGCTTTATCACCACAAAAGCTGACGTTCATA
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIIIHHHIIIIIIIIIIIGHIHIIIIIEHHHGHHIICHEHEH07F@HIHFC@CHDHHIHHIIHIIEHHIEECGHHE?GH@.@@FEA.7@FEH."""
self.assertEqual(result, expected)
def test_EmptyRecord_EmptyString(self):
result = bam2fastq.to_fastq_string(pysam.AlignedSegment())
expected = ""
self.assertEqual(result, expected)