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Followup fixup the chromosome zarr encoding bug #11

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Merged
ravwojdyla merged 2 commits into from
Jun 19, 2025
Merged

Followup fixup the chromosome zarr encoding bug #11

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3174aa9
Add error traceback
ravwojdyla Jun 19, 2025
648cdeb
Fixup chromosome name take 2
ravwojdyla Jun 19, 2025
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8 changes: 6 additions & 2 deletions src/caduceus_inf.py
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Original file line number Diff line number Diff line change
@@ -1,8 +1,11 @@
import argparse
import os
import sys
import time
import traceback
from typing import Any, Literal

import numpy as np
import torch
import torch.nn as nn
import xarray as xr
Expand Down Expand Up @@ -212,7 +215,8 @@ def generate_soft_labels(
"sample": batch_indices,
"sequence": range(input_ids.shape[1]),
"vocab": range(logits.shape[-1]),
"chr_name": (["sample"], list(chr_names)),
# NOTE: use U5 encoding because chr name can be either 3 or 4 characters long, e.g. `chr1` or `chr10`
"chr_name": (["sample"], np.asarray(list(chr_names)).astype("<U5")),
"start": (["sample"], [int(s) for s in starts]),
"end": (["sample"], [int(e) for e in ends]),
},
Expand Down Expand Up @@ -275,7 +279,7 @@ def generate_soft_labels(

except Exception as e:
was_interrupted = True
print(f"\nError occurred: {str(e)}")
print(f"\n{traceback.format_exc()}\nError occurred: {str(e)}", file=sys.stderr)

finally:
if nvml_available and pynvml is not None:
Expand Down