Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add query to ref coord mapping #120

Open
wants to merge 4 commits into
base: master
Choose a base branch
from
Open

Add query to ref coord mapping #120

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
5b55e6b
add query to ref coord mapping
chilampoon Oct 10, 2023
3c807bb
rm redundant interpolation
chilampoon Oct 11, 2023
804fb9b
change N ref ops to false
chilampoon Oct 12, 2023
a62f46d
intron aware extract_ref_reg
chilampoon Oct 15, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion src/remora/data_chunks.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@
[True, False, False, False, False, False, False, True, True]
)
QUERY_OPS = np.array([True, True, False, False, True, False, False, True, True])
REF_OPS = np.array([True, False, True, True, False, False, False, True, True])
REF_OPS = np.array([True, False, True, False, False, False, False, True, True])
CIGAR_CODES = ["M", "I", "D", "N", "S", "H", "P", "=", "X"]
CODE_TO_OP = {
"M": 0,
Expand Down
36 changes: 30 additions & 6 deletions src/remora/io.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -492,6 +492,24 @@ def compute_base_space_sig_coords(seq_to_sig_map):
np.arange(seq_to_sig_map.size),
)

REF_OPS = np.array([True, False, True, True, False, False, False, True, True])
REFSEQ_OPS = np.array([True, False, True, False, False, False, False, True, True])
def get_ref_seq_pos(cigar, ref_start):
'''
Map query base to reference coordinates (0-based)
Returns
array shape (ref_len,); ref_len = len(aln.get_reference_sequences())
'''
ops, lens = map(np.array, zip(*cigar))
starts = np.cumsum(np.where(REF_OPS[ops], lens, 0)) - np.where(REF_OPS[ops], lens, 0)
ranges = [
np.arange(start, start + l)
for op, start, l in zip(ops, starts, lens)
if REFSEQ_OPS[op]
]
ref_coords = ref_start + np.concatenate(ranges)
return ref_coords


@dataclass
class ReadRefReg:
Expand Down Expand Up @@ -1532,6 +1550,8 @@ def add_alignment(
)
self.ref_seq = None
self.cigar = alignment_record.cigartuples
self.ref_pos = get_ref_seq_pos(self.cigar, self.ref_reg.start)
self.ref_pos = np.concatenate([self.ref_pos, [self.ref_pos[-1]+1]])
if alignment_record.is_reverse:
if self.ref_seq is not None:
self.ref_seq = util.revcomp(self.ref_seq)
Expand All @@ -1546,7 +1566,7 @@ def add_alignment(
"discordant ref seq lengths: move+cigar:"
f"{self.ref_to_signal.size} ref_seq:{len(self.ref_seq)}"
)
self.ref_reg.end = self.ref_reg.start + self.ref_to_signal.size - 1
self.ref_reg.end = alignment_record.reference_end

@classmethod
def from_pod5_and_alignment(
Expand Down Expand Up @@ -1757,17 +1777,21 @@ def extract_ref_reg(self, ref_reg):
raise RemoraError(
"Cannot extract reference region from unmapped read"
)
if ref_reg.start >= self.ref_reg.start + self.ref_seq_len:
if ref_reg.start >= self.ref_reg.end:
raise RemoraError("Reference region starts after read ends")
if ref_reg.end < self.ref_reg.start:
raise RemoraError("Reference region ends before read starts")

reg_within_read = self.ref_pos[(self.ref_pos >= ref_reg.start) & (self.ref_pos <= ref_reg.end)]
st_idx, = np.where(self.ref_pos == min(reg_within_read))
en_idx, = np.where(self.ref_pos == max(reg_within_read))

if self.ref_reg.strand == "+":
reg_st_within_read = max(0, ref_reg.start - self.ref_reg.start)
reg_en_within_read = ref_reg.end - self.ref_reg.start
reg_st_within_read = st_idx[0]
reg_en_within_read = en_idx[0]
else:
reg_st_within_read = max(0, self.ref_reg.end - ref_reg.end)
reg_en_within_read = self.ref_reg.end - ref_reg.start
reg_st_within_read = en_idx[0]
reg_en_within_read = st_idx[0]
reg_seq_to_sig = self.ref_to_signal[
reg_st_within_read : reg_en_within_read + 1
].copy()
Expand Down