def construct_hg38_map(n2nl_aln, hg38_bam):
"""Constructs a map of hg38 position -> sequence alignment position -> MSA position"""
# construct sequence alignment position -> MSA position map using the MSA
aln_f = Fasta(n2nl_aln)
seq_aln_map = defaultdict(dict)
for name, seq in aln_f.iteritems():
seq_pos = 0
for aln_pos, x in enumerate(str(seq)):
seq_aln_map[name][seq_pos] = aln_pos
if x != '-':
seq_pos += 1
# find maximum position for reversing negative strand
max_pos = {x: max(y.keys()) for x, y in seq_aln_map.iteritems()}
# construct a hg38 -> sequence positions using the sequences trivially mapped back to hg38
hg38_map = {}
for rec in pysam.Samfile(hg38_bam):
m = {y: x for x, y in rec.aligned_pairs}
# invert positions for negative strand genes
if rec.qname in ['NOTCH2', 'NOTCH2NL-A', 'NOTCH2NL-B']:
m = {x: max_pos[rec.qname] - y for x, y in m.iteritems()}
hg38_map[rec.qname] = m
# construct a table mapping each alignment position to all hg38 positions
r = defaultdict(dict)
for name, pos_map in hg38_map.iteritems():
for hg38_pos, seq_pos in pos_map.iteritems():
aln_pos = seq_aln_map[name][seq_pos]
r[name][aln_pos] = hg38_pos
# now invert this map, so that we have our hg38 -> aln map
final_map = {}
for name in r:
for aln_pos in r[name]:
hg38_pos = r[name][aln_pos]
assert hg38_pos not in final_map
final_map[hg38_pos] = aln_pos
return final_map
from collections import *
from tools.intervals import *
from tools.misc import *
from tools.procOps import *
from tools.fileOps import *
from tools.bio import *
from tools.psl import *
from itertools import *
import bisect
# In[5]:
# first, construct a map of sequence positions to alignment positions
aln_f = Fasta('notch2nl_alignment.fa')
seq_aln_map = defaultdict(dict)
for name, seq in aln_f.iteritems():
seq_pos = 0
for aln_pos, x in enumerate(str(seq)):
seq_aln_map[name][seq_pos] = aln_pos
if x != '-':
seq_pos += 1
# In[182]:
# find maximum position for reversing negative strand
max_pos = {x: max(y.keys()) for x, y in seq_aln_map.iteritems()}
# In[193]:
# next, construct a map of hg38 positions to sequence positions using the alignment
hg38_map = {}
