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Bug fix and couple minor improvements #95

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Bug fix and couple minor improvements #95

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2f56e30
Major bug fix: fastq output read2 == read1
tprodanov Sep 13, 2021
aa8987e
Ignore chromosomes not in input regions
tprodanov Sep 13, 2021
74a67b8
Speed up N-region modification
tprodanov Sep 13, 2021
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7 changes: 6 additions & 1 deletion gen_reads.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
#!/usr/bin/env source
#!/usr/bin/env python3
# encoding: utf-8
""" ////////////////////////////////////////////////////////////////////////////////
/// ///
Expand Down Expand Up @@ -405,8 +405,13 @@ def main(raw_args=None):
# keep track of the number of reads we've sampled, for read-names
read_name_count = 1
unmapped_records = []
skip_chromosomes = off_target_scalar == 0.0 or off_target_discard

for chrom in range(len(ref_index)):
chrom_name = ref_index[chrom][0]
if input_regions and chrom_name not in input_regions and skip_chromosomes:
# print('Skipping {}'.format(chrom_name))
continue

# read in reference sequence and notate blocks of Ns
(ref_sequence, n_regions) = read_ref(reference, ref_index[chrom], n_handling)
Expand Down
3 changes: 2 additions & 1 deletion source/output_file_writer.py
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Expand Up @@ -183,8 +183,9 @@ def write_fastq_record(self, read_name, read1, qual1, read2=None, qual2=None, or
if read2 is not None and orientation is True:
(read2, quality2) = (read2.reverse_complement(), qual2[::-1])
elif read2 is not None and orientation is False:
prev_read1 = read1
(read1, quality1) = (read2.reverse_complement(), qual2[::-1])
(read2, quality2) = (read1, qual1)
(read2, quality2) = (prev_read1, qual1)

if self.fasta_instead:
self.fq1_buffer.append('>' + read_name + '/1\n' + str(read1) + '\n')
Expand Down
4 changes: 2 additions & 2 deletions source/ref_func.py
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Original file line number Diff line number Diff line change
Expand Up @@ -132,10 +132,10 @@ def read_ref(ref_path, ref_inds_i, n_handling, n_unknowns=True, quiet=False):
for region in n_atlas:
n_info['all'].extend(region)
if region[1] - region[0] <= n_handling[1]:
temp = my_dat.tomutable()
for i in range(region[0], region[1]):
temp = my_dat.tomutable()
temp[i] = random.choice(ALLOWED_NUCL)
my_dat = temp.toseq()
my_dat = temp.toseq()
else:
n_info['big'].extend(region)
elif n_handling[0] == 'allChr' and n_handling[2] in OK_CHR_ORD:
Expand Down