From a4acdf778aa90427f2548923c68a0040f271aa25 Mon Sep 17 00:00:00 2001
From: Yenaled <delaneyk.sullivan@gmail.com>
Date: Fri, 5 Jan 2024 06:53:37 -0800
Subject: [PATCH] cleanup anndata

also clean up args.umi_gene legacy
---
 kb_python/count.py | 10 ----------
 kb_python/main.py  |  2 +-
 2 files changed, 1 insertion(+), 11 deletions(-)

diff --git a/kb_python/count.py b/kb_python/count.py
index 3cdc449..bf5d328 100755
--- a/kb_python/count.py
+++ b/kb_python/count.py
@@ -2016,29 +2016,24 @@ def update_results_with_suffix(current_results, new_results, suffix):
             if sum_matrices and sum_matrices != 'none':
                 # Sum up multiple matrices
                 sums = {}
-                updated_prefixes = []
                 if sum_matrices == 'cell' or sum_matrices == 'total':
                     sums['cell'] = do_sum_matrices(
                         count_result[prefixes.index('processed')]['mtx'],
                         count_result[prefixes.index('ambiguous')]['mtx'],
                         f'{counts_prefix}.cell.mtx', em or mm
                     )
-                    updated_prefixes = ['cell', 'unprocessed']
                 if sum_matrices == 'nucleus' or sum_matrices == 'total':
                     sums['nucleus'] = do_sum_matrices(
                         count_result[prefixes.index('unprocessed')]['mtx'],
                         count_result[prefixes.index('ambiguous')]['mtx'],
                         f'{counts_prefix}.nucleus.mtx', em or mm
                     )
-                    updated_prefixes = ['processed', 'nucleus']
                 if sum_matrices == 'total':
                     sums['total'] = do_sum_matrices(
                         f'{counts_prefix}.mature.mtx',
                         f'{counts_prefix}.nucleus.mtx',
                         f'{counts_prefix}.total.mtx', em or mm
                     )
-                    updated_prefixes = prefixes
-                prefixes = updated_prefixes
                 for prefix, f in sums.items():
                     res = copy.deepcopy(count_result[0])
                     res['mtx'] = f
@@ -2184,29 +2179,24 @@ def update_results_with_suffix(current_results, new_results, suffix):
             if sum_matrices and sum_matrices != 'none':
                 # Sum up multiple matrices
                 sums = {}
-                updated_prefixes = []
                 if sum_matrices == 'cell' or sum_matrices == 'total':
                     sums['cell'] = do_sum_matrices(
                         count_result[prefixes.index('processed')]['mtx'],
                         count_result[prefixes.index('ambiguous')]['mtx'],
                         f'{filtered_counts_prefix}.cell.mtx', em or mm
                     )
-                    updated_prefixes = ['cell', 'unprocessed']
                 if sum_matrices == 'nucleus' or sum_matrices == 'total':
                     sums['nucleus'] = do_sum_matrices(
                         count_result[prefixes.index('unprocessed')]['mtx'],
                         count_result[prefixes.index('ambiguous')]['mtx'],
                         f'{filtered_counts_prefix}.nucleus.mtx', em or mm
                     )
-                    updated_prefixes = ['processed', 'nucleus']
                 if sum_matrices == 'total':
                     sums['total'] = do_sum_matrices(
                         f'{filtered_counts_prefix}.mature.mtx',
                         f'{filtered_counts_prefix}.nucleus.mtx',
                         f'{filtered_counts_prefix}.total.mtx', em or mm
                     )
-                    updated_prefixes = prefixes
-                prefixes = updated_prefixes
                 for prefix, f in sums.items():
                     res = copy.deepcopy(count_result[0])
                     res['mtx'] = f
diff --git a/kb_python/main.py b/kb_python/main.py
index 9c7d776..683ef3f 100755
--- a/kb_python/main.py
+++ b/kb_python/main.py
@@ -689,7 +689,7 @@ def parse_count(
                 fragment_s=args.fragment_s,
                 paired=args.parity == 'paired',
                 strand=args.strand,
-                umi_gene=args.umi_gene,
+                umi_gene=args.x.upper() not in ('BULK', 'SMARTSEQ2'),
                 em=args.em,
                 by_name=args.gene_names
             )