merge from main

.github/workflows/main.yml

@@ -18,7 +18,7 @@ jobs:
 
       - name: Install Mamba
         run: |
-          conda install -c conda-forge mamba=1.5.12 -y
+          conda install -c conda-forge mamba=1.5.12 -y 
           
       - name: Print conda folder contents
         run: |

src/utils.py

@@ -14,6 +14,7 @@
 from multiprocessing import Pool
 import multiprocessing
 import time
+import tracemalloc
 import anndata as ad
 import scanpy as sc
 from scipy.sparse import csr_matrix
@@ -1460,7 +1461,8 @@ def get_edits_with_coverage_df(output_folder,
     # this will still be true even with no barcode specified, in which case the contig will be <contig>_no_barcode
 
     # Therefore: replace the contig with the part before the barcode
-    all_edit_info_unique_position_with_coverage_df['contig'] = all_edit_info_unique_position_with_coverage_df.apply(lambda row: row['contig'].replace('_{}'.format(row['barcode']), ''), axis=1)
+    if len(all_edit_info_unique_position_with_coverage_df) > 0:
+        all_edit_info_unique_position_with_coverage_df['contig'] = all_edit_info_unique_position_with_coverage_df.apply(lambda row: row['contig'].replace('_{}'.format(row['barcode']), ''), axis=1)
 
     return all_edit_info_unique_position_with_coverage_df
 

tests/integration_tests_auto_check.py

@@ -8,7 +8,12 @@
 
 
 test_name_to_expectations = {
-"edge_case_test": {
+    "no_edits_edge_case_test": {
+        "folder": "strandedness_tests",
+        "total_edit_sites": 0,
+        "expectations": []
+    },
+    "edge_case_test": {
         "folder": "singlecell_tests",
         "total_edit_sites": 2,
         "expectations": [{

tests/integration_tests_run.sh

@@ -1,3 +1,6 @@
+#!/bin/bash
+set -e  # Exit immediately if a command exits with a non-zero status
+
 mypython=$1
 
 echo "Python is $mypython"
@@ -13,11 +16,11 @@ tests_folder="strandedness_tests/"
 echo "Bulk tests scripts"
 ls -lh $MARINE/tests/$tests_folder/scripts/
 
-for t in "F1R2_pair_test-single_end_mode_sailor" "F1R2_pair_test-single_end_mode" "F1R2_pair_test" "F2R1_end_second_in_pair_test" "same_pos_dif_reads_test" "tax1bp3_chr17_3665556_read_test" "pair_test" "unstranded_pair_test"
+for t in "no_edits_edge_case_test" "F1R2_pair_test-single_end_mode_sailor" "F1R2_pair_test-single_end_mode" "F1R2_pair_test" "F2R1_end_second_in_pair_test" "same_pos_dif_reads_test" "tax1bp3_chr17_3665556_read_test" "pair_test" "unstranded_pair_test"
 do
     echo $t
     echo "Removing old files..."
-    rm $MARINE/tests/$tests_folder$t/* -r
+    rm $MARINE/tests/$tests_folder$t/* -r || true
 
     echo "Running tests..."
     bash $MARINE/tests/$tests_folder/scripts/$t.sh $mypython
@@ -39,7 +42,7 @@ for t in "only_5_cells_test" "only_5_cells_bulk_mode_test" "only_5_cells_all_cel
 do
     echo $t
     echo "Removing old files..."
-    rm $MARINE/tests/$tests_folder$t/* -r
+    rm $MARINE/tests/$tests_folder$t/* -r || true
 
     echo "Running tests..."
     bash $MARINE/tests/$tests_folder/scripts/$t.sh $mypython
@@ -53,4 +56,4 @@ $mypython $MARINE/tests/integration_tests_auto_check.py tests
 exitcode=$?
 
 echo "Exit code: $exitcode"
-exit $exitcode
+exit $exitcode

tests/strandedness_tests/scripts/no_edits_edge_case_test.sh

@@ -0,0 +1,20 @@
+mypython=$1
+
+$mypython $MARINE/marine.py \
+--bam_filepath \
+$MARINE/tests/strandedness_tests/bams/same_pos_dif_reads.bam \
+--annotation_bedfile_path \
+$MARINE/annotations/hg38_gencode.v35.annotation.genes.bed \
+--output_folder \
+$MARINE/tests/strandedness_tests/no_edits_edge_case_test \
+--min_dist_from_end \
+0 \
+--min_base_quality \
+50 \
+--cores \
+16 \
+--paired_end \
+--strandedness 2 \
+--contigs "chr17" \
+--num_intervals_per_contig 16 \
+--keep_intermediate_files