"""
Investigating the region of NUDT4P near Notch2NL-A that appears to have segregating
deletions.
"""
roi = ['chr1', 146231874, 146358436]
na12878_bam = '/hive/users/ifiddes/longranger-1.2.0/NA12878_combined/outs/phased_possorted_bam.bam'
import pysam
import numpy as np
from extract_linked_bams import bin_reads
bam_handle = pysam.Samfile(na12878_bam)
reads = bin_reads(roi[0], roi[1], roi[2], bam_handle, offset=10000)
# 4730 tags
# now, I want to grab any read with these tags, mapped or unmapped.
def eval_rec(rec, read_dict):
tags = dict(rec.tags)
if 'BX' in tags:
t = tags['BX']
if t in read_dict:
read_dict[t].append(rec)
full_reads = reads.copy()
for rec in bam_handle.fetch(until_eof=True):
eval_rec(rec, full_reads)
"""
Investigating the region of NUDT4P near Notch2NL-A that appears to have segregating
deletions.
"""
roi = ['chr1', 146231874, 146358436]
na12878_bam = '/hive/users/ifiddes/longranger-1.2.0/NA12878_combined/outs/phased_possorted_bam.bam'
import pysam
import numpy as np
from extract_linked_bams import bin_reads
bam_handle = pysam.Samfile(na12878_bam)
reads = bin_reads(roi[0], roi[1], roi[2], bam_handle, offset=10000)
# 4730 tags
# now, I want to grab any read with these tags, mapped or unmapped.
def eval_rec(rec, read_dict):
tags = dict(rec.tags)
if 'BX' in tags:
t = tags['BX']
if t in read_dict:
read_dict[t].append(rec)
full_reads = reads.copy()
for rec in bam_handle.fetch(until_eof=True):
eval_rec(rec, full_reads)
"""
Attempt to construct unitigs out of reads in the region and map them back to the reference
"""
roi = ['chr1', 145966000, 146510000]
na12878_bam = '/hive/users/ifiddes/longranger-1.2.0/NA12878_combined/outs/phased_possorted_bam.bam'
import pysam
import numpy as np
from collections import defaultdict
from extract_linked_bams import bin_reads
bam_handle = pysam.Samfile(na12878_bam)
unitig_region_mapped_reads = bin_reads(roi[0], roi[1], roi[2], bam_handle, offset=10000)
def eval_rec(rec, read_dict):
tags = dict(rec.tags)
if 'BX' in tags:
t = tags['BX']
if t in read_dict:
read_dict[t].append(rec)
# now bring in the unmapped reads
unmapped_bam = '/hive/users/ifiddes/longranger-1.2.0/NA12878_combined/outs/unmapped.bam'
unitig_region_mapped_and_unmapped_reads = unitig_region_mapped_reads.copy()
unmapped_handle = pysam.Samfile(unmapped_bam)
for rec in unmapped_handle.fetch(until_eof=True):
eval_rec(rec, unitig_region_mapped_and_unmapped_reads)
