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Merged
zktuong merged 1 commit into from
Aug 14, 2026
+14 −2
Merged

minimum umi filtering #674

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6 changes: 6 additions & 0 deletions src/dandelion/base/preprocessing/_preprocessing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2866,6 +2866,7 @@ def check_contigs(
adata: AnnData | None = None,
productive_only: bool = True,
library_type: Literal["ig", "tr-ab", "tr-gd"] | None = None,
min_umi: int = 1,
umi_foldchange_cutoff: int = 2,
consensus_foldchange_cutoff: int = 5,
ntop_vdj: int = 1,
Expand Down Expand Up @@ -2921,6 +2922,8 @@ def check_contigs(
TRA, TRB
`tr-gd`:
TRG, TRD
min_umi : int, optional
Minimum UMI count for a contig to be considered.
umi_foldchange_cutoff : int, optional
related to minimum fold change of UMI count, required to rescue contigs/barcode otherwise they will be marked as extra/ambiguous.
consensus_foldchange_cutoff : int, optional
Expand Down Expand Up @@ -2986,6 +2989,9 @@ def check_contigs(
else:
dat = dat_.copy()

# filter based on umi
dat = dat[dat["umi_count"].astype(int) >= min_umi].copy()

if acceptable is not None:
dat = dat[dat.locus.isin(acceptable)].copy()

Expand Down
10 changes: 8 additions & 2 deletions src/dandelion/polars/preprocessing/_preprocessing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4213,6 +4213,7 @@ def check_contigs(
adata: AnnData | None = None,
productive_only: bool = True,
library_type: Literal["ig", "tr-ab", "tr-gd"] | None = None,
min_umi: int = 1,
umi_foldchange_cutoff: float = 2.0,
consensus_foldchange_cutoff: float = 5.0,
ntop_vdj: int = 1,
Expand Down Expand Up @@ -4247,6 +4248,8 @@ def check_contigs(
- `ig`: IGH, IGK, IGL
- `tr-ab`: TRA, TRB
- `tr-gd`: TRG, TRD
min_umi : int, optional
Minimum UMI count for a contig to be considered.
umi_foldchange_cutoff : float, default=2.0
Minimum UMI fold-change threshold for dominance test.
consensus_foldchange_cutoff : float, default=5.0
Expand Down Expand Up @@ -4323,8 +4326,6 @@ def check_contigs(
mark_ambiguous_contigs_vec : Core vectorized function for marking contigs
check_chimeric_genes_vec : Detects chimeric gene calls
"""
from pathlib import Path
import os

if verbose:
print("Filtering contigs...")
Expand Down Expand Up @@ -4384,6 +4385,11 @@ def check_contigs(
else:
dat = dat_

# filter by minimum UMI count (lazy)
dat = dat.filter(
pl.col("umi_count").cast(pl.Int64) >= min_umi
) # if the row has no umi_count, it will be filtered out since it will be null and null >= min_umi is false

# Filter by library type (lazy)
if acceptable is not None:
dat = dat.filter(pl.col("locus").is_in(acceptable))
Expand Down
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