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Correct typing for barcode_dcretc_list #47

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Merged
mvcowley merged 1 commit into from
Feb 23, 2026
Merged

Correct typing for barcode_dcretc_list #47

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20 changes: 10 additions & 10 deletions src/decombinator/collapse.py
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Original file line number Diff line number Diff line change
Expand Up @@ -64,7 +64,6 @@
import polyleven
import pyrepseq.nn as prsnn
import regex
import scipy.sparse
from scipy import sparse

########################################################################################################################
Expand Down Expand Up @@ -648,15 +647,15 @@ def read_in_data(

def create_clustering_objs(
barcode_dcretc: dict[str, list[str]],
) -> tuple[int, list[tuple[str, str]], list[tuple[str, str]]]:
) -> tuple[int, list[tuple[str, list[str]]], list[tuple[str, str]]]:

# get number of initial groups
num_initial_groups = len(barcode_dcretc)

# convert barcode_dcretc collection to list format
barcode_dcretc_list = []
for _, (j, k) in enumerate(barcode_dcretc.items()):
barcode_dcretc_list.append((j, k))
for key, value in barcode_dcretc.items():
barcode_dcretc_list.append((key, value))

umi_protoseq_tuple = [
(x[0].split("|")[0], x[0].split("|")[2]) for x in barcode_dcretc_list
Expand Down Expand Up @@ -698,7 +697,7 @@ def make_merge_groups(

def make_clusters(
merge_groups: sparse.coo_matrix,
barcode_dcretc: list[tuple[str, list[str]]],
barcode_dcretc_list: list[tuple[str, list[str]]],
seq_threshold: int,
) -> coll.defaultdict[str, list[str]]:
# Considers clusters as an undirected graph composed of disconnected subgraphs.
Expand All @@ -719,8 +718,8 @@ def make_clusters(

for i, j in zip(merge_groups.row, merge_groups.col):
protoseqs = [
barcode_dcretc[i][0].split("|")[2],
barcode_dcretc[j][0].split("|")[2],
barcode_dcretc_list[i][0].split("|")[2],
barcode_dcretc_list[j][0].split("|")[2],
]
if are_seqs_equivalent(
protoseqs[0], protoseqs[1], percent_seq_threshold
Expand All @@ -736,15 +735,16 @@ def make_clusters(
for subgraph in con_comp:
# get full barcode barcode information of the first node in the subgraph from barcode_dcretc
# this will be serve as the dictionary key for the cluster
base_node_barcode = barcode_dcretc[list(subgraph)[0]][0]
# will be the lowest index number in the component
base_node_barcode = barcode_dcretc_list[list(subgraph)[0]][0]

# get the full sequence information of each node in the subgraph from barcode_dcretc and
# add them to cluster collection with a cluster representative barcode (base_node_barcode)
for k in list(subgraph):
clusters[base_node_barcode] += barcode_dcretc[k][1]
clusters[base_node_barcode] += barcode_dcretc_list[k][1]

# add remaining barcode/protoseqs that do not need merging to the clusters
for i, bdcretc in enumerate(barcode_dcretc):
for i, bdcretc in enumerate(barcode_dcretc_list):
# if already accounted for in the merged_groups then skip over
if i in G.nodes:
continue
Expand Down