def _break_reads(self, contig, position, fout, min_read_length=250):
'''Get all reads from contig, but breaks them all at given position (0-based) in the reference. Writes to fout. Currently pproximate where it breaks (ignores indels in the alignment)'''
sam_reader = pysam.Samfile(self.bam, "rb")
for read in sam_reader.fetch(contig):
seqs = []
if read.pos < position < read.reference_end - 1:
split_point = position - read.pos
if split_point - 1 >= min_read_length:
sequence = mapping.aligned_read_to_read(
read, revcomp=False,
ignore_quality=not self.fastq_out).subseq(
0, split_point)
sequence.id += '.left'
seqs.append(sequence)
if read.query_length - split_point >= min_read_length:
sequence = mapping.aligned_read_to_read(
read, revcomp=False,
ignore_quality=not self.fastq_out).subseq(
split_point, read.query_length)
sequence.id += '.right'
seqs.append(sequence)
else:
seqs.append(
mapping.aligned_read_to_read(
read, revcomp=False,
ignore_quality=not self.fastq_out))
for seq in seqs:
if read.is_reverse:
seq.revcomp()
print(seq, file=fout)
def test_aligned_read_to_read(self):
'''test aligned_read_to_read'''
infile = os.path.join(data_dir,
'mapping_test_aligned_read_to_read.bam')
sam_reader = pysam.Samfile(infile, "rb")
aln1, aln2 = [x for x in sam_reader.fetch()]
read1_fq = pyfastaq.sequences.Fastq(
'read1',
'TGTGTAACACTCCACCTCTGGTTCCCAGAGTTCGGTATCCGGCCGATACTTGAGGATAGC',
'IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGHFEDCBA')
read1_fa = pyfastaq.sequences.Fasta(
'read1',
'TGTGTAACACTCCACCTCTGGTTCCCAGAGTTCGGTATCCGGCCGATACTTGAGGATAGC')
self.assertEqual(read1_fq, mapping.aligned_read_to_read(aln1))
self.assertEqual(read1_fq,
mapping.aligned_read_to_read(aln1, revcomp=False))
self.assertEqual(
read1_fa, mapping.aligned_read_to_read(aln1, ignore_quality=True))
read2 = pyfastaq.sequences.Fastq(
'read2',
'GATCGTCACGAAAGAACCAAGCCGGATCGTGGGAGGGGTACAACTCAGGTGAATTAACGT',
'HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGFEDC')
read2_rev = copy.copy(read2)
read2_rev.revcomp()
self.assertEqual(read2, mapping.aligned_read_to_read(aln2))
self.assertEqual(read2_rev,
mapping.aligned_read_to_read(aln2, revcomp=False))
def _all_reads_from_contig(self, contig, fout):
'''Gets all reads from contig called "contig" and writes to fout'''
sam_reader = pysam.Samfile(self.bam, "rb")
for read in sam_reader.fetch(contig):
print(mapping.aligned_read_to_read(
read, ignore_quality=not self.fastq_out),
file=fout)
def _get_region(self, contig, start, end, fout, min_length=250):
'''Writes reads mapping to given region of contig, trimming part of read not in the region'''
sam_reader = pysam.Samfile(self.bam, "rb")
trimming_end = (start == 0)
for read in sam_reader.fetch(contig, start, end):
read_interval = pyfastaq.intervals.Interval(
read.pos, read.reference_end - 1)
seq = mapping.aligned_read_to_read(
read, ignore_quality=not self.fastq_out, revcomp=False)
if trimming_end:
bases_off_start = 0
bases_off_end = max(0, read.reference_end - 1 - end)
#seq.seq = seq.seq[:read.query_alignment_end - bases_off_end]
seq = seq.subseq(0, read.query_alignment_end - bases_off_end)
else:
bases_off_start = max(0, start - read.pos + 1)
#seq.seq = seq.seq[bases_off_start + read.query_alignment_start:]
seq = seq.subseq(bases_off_start + read.query_alignment_start,
len(seq))
if read.is_reverse:
seq.revcomp()
if len(seq) >= min_length:
print(seq, file=fout)
def _get_all_unmapped_reads(self, fout):
'''Writes all unmapped reads to fout'''
sam_reader = pysam.Samfile(self.bam, "rb")
for read in sam_reader.fetch(until_eof=True):
if read.is_unmapped:
print(mapping.aligned_read_to_read(read, ignore_quality=True),
file=fout)
def test_aligned_read_to_read(self):
'''test aligned_read_to_read'''
infile = os.path.join(data_dir, 'mapping_test_aligned_read_to_read.bam')
sam_reader = pysam.Samfile(infile, "rb")
aln1, aln2 = [x for x in sam_reader.fetch()]
read1_fq = pyfastaq.sequences.Fastq('read1', 'TGTGTAACACTCCACCTCTGGTTCCCAGAGTTCGGTATCCGGCCGATACTTGAGGATAGC', 'IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGHFEDCBA')
read1_fa = pyfastaq.sequences.Fasta('read1', 'TGTGTAACACTCCACCTCTGGTTCCCAGAGTTCGGTATCCGGCCGATACTTGAGGATAGC')
self.assertEqual(read1_fq, mapping.aligned_read_to_read(aln1))
self.assertEqual(read1_fq, mapping.aligned_read_to_read(aln1, revcomp=False))
self.assertEqual(read1_fa, mapping.aligned_read_to_read(aln1, ignore_quality=True))
read2 = pyfastaq.sequences.Fastq('read2', 'GATCGTCACGAAAGAACCAAGCCGGATCGTGGGAGGGGTACAACTCAGGTGAATTAACGT', 'HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGFEDC')
read2_rev = copy.copy(read2)
read2_rev.revcomp()
self.assertEqual(read2, mapping.aligned_read_to_read(aln2))
self.assertEqual(read2_rev, mapping.aligned_read_to_read(aln2, revcomp=False))
def _exclude_region(self, contig, start, end, fout):
'''Writes reads not mapping to the given region of contig, start and end as per python convention'''
sam_reader = pysam.Samfile(self.bam, "rb")
exclude_interval = pyfastaq.intervals.Interval(start, end - 1)
for read in sam_reader.fetch(contig):
read_interval = pyfastaq.intervals.Interval(read.pos, read.reference_end - 1)
if not read_interval.intersects(exclude_interval):
print(mapping.aligned_read_to_read(read, ignore_quality=True), file=fout)
def _exclude_region(self, contig, start, end, fout):
'''Writes reads not mapping to the given region of contig, start and end as per python convention'''
sam_reader = pysam.Samfile(self.bam, "rb")
exclude_interval = pyfastaq.intervals.Interval(start, end - 1)
for read in sam_reader.fetch(contig):
read_interval = pyfastaq.intervals.Interval(
read.pos, read.reference_end - 1)
if not read_interval.intersects(exclude_interval):
print(mapping.aligned_read_to_read(read, ignore_quality=True),
file=fout)
def _break_reads(self, contig, position, fout, min_read_length=250):
'''Get all reads from contig, but breaks them all at given position (0-based) in the reference. Writes to fout. Currently pproximate where it breaks (ignores indels in the alignment)'''
sam_reader = pysam.Samfile(self.bam, "rb")
for read in sam_reader.fetch(contig):
seqs = []
if read.pos < position < read.reference_end - 1:
split_point = position - read.pos
if split_point - 1 >= min_read_length:
sequence = mapping.aligned_read_to_read(read, revcomp=False, ignore_quality=True).subseq(0, split_point)
sequence.id += '.left'
seqs.append(sequence)
if read.query_length - split_point >= min_read_length:
sequence = mapping.aligned_read_to_read(read, revcomp=False, ignore_quality=True).subseq(split_point, read.query_length)
sequence.id += '.right'
seqs.append(sequence)
else:
seqs.append(mapping.aligned_read_to_read(read, revcomp=False, ignore_quality=True))
for seq in seqs:
if read.is_reverse:
seq.revcomp()
print(seq, file=fout)
def _get_region(self, contig, start, end, fout, min_length=250):
'''Writes reads mapping to given region of contig, trimming part of read not in the region'''
sam_reader = pysam.Samfile(self.bam, "rb")
trimming_end = (start == 0)
for read in sam_reader.fetch(contig, start, end):
read_interval = pyfastaq.intervals.Interval(read.pos, read.reference_end - 1)
seq = mapping.aligned_read_to_read(read, ignore_quality=True, revcomp=False)
if trimming_end:
bases_off_start = 0
bases_off_end = max(0, read.reference_end - 1 - end)
seq.seq = seq.seq[:read.query_alignment_end - bases_off_end]
else:
bases_off_start = max(0, start - read.pos + 1)
seq.seq = seq.seq[bases_off_start + read.query_alignment_start:]
if read.is_reverse:
seq.revcomp()
if len(seq) >= min_length:
print(seq, file=fout)
def _get_all_unmapped_reads(self, fout):
'''Writes all unmapped reads to fout'''
sam_reader = pysam.Samfile(self.bam, "rb")
for read in sam_reader.fetch(until_eof=True):
if read.is_unmapped:
print(mapping.aligned_read_to_read(read, ignore_quality=True), file=fout)
def _all_reads_from_contig(self, contig, fout):
'''Gets all reads from contig called "contig" and writes to fout'''
sam_reader = pysam.Samfile(self.bam, "rb")
for read in sam_reader.fetch(contig):
print(mapping.aligned_read_to_read(read, ignore_quality=True), file=fout)
