Add support for 5v3, the previous argument 5v3 is actually for 5v2.

blaze/config.py

@@ -34,8 +34,9 @@
 DEFAULT_UMI_SIZE= 12 if DEFAULT_GRB_KIT=='v3' else 10
 
 # The 10X barcode whitelists has been packed in the package
-DEFAULT_GRB_WHITELIST_V3=os.path.join(os.path.dirname(__file__), '10X_bc', '3M-february-2018.zip')
+DEFAULT_GRB_WHITELIST_3V3=os.path.join(os.path.dirname(__file__), '10X_bc', '3M-february-2018.zip')
 DEFAULT_GRB_WHITELIST_V2=os.path.join(os.path.dirname(__file__), '10X_bc', '737K-august-2016.txt')
+DEFAULT_GRB_WHITELIST_5V3=os.path.join(os.path.dirname(__file__), '10X_bc', '3M-5pgex-jan-2023.zip')
 
 #output
 DEFAULT_GRB_OUT_RAW_BC='putative_bc.csv'

blaze/main.py

@@ -88,8 +88,8 @@ def print_help():
                     Maximum edit distance allowed between a putative barcode and a barcode 
                     for a read/putative barcdoe to be assigned to the barcode. Default: --max-edit-distance {DEFAULT_ASSIGNMENT_ED}
                 
-                --kit-version <3v2 or 3v3 or 5v3>:
-                    Choose from 10X Single Cell 3ʹ gene expression v2 or v3 or 5' gene expression. If using other
+                --kit-version <3v2 3v3 5v2 or 5v3>:
+                    Choose from 10X Single Cell 3ʹ gene expression v2 or v3 or 5' gene expression v2 or v3. If using other
                     protocols, please do not specify this option and specify --full-bc-whitelist instead. By default, 
                     `--kit_version v3`  will be used if --full-bc-whitelist is not specified.
 
@@ -223,19 +223,21 @@ def print_help():
     out_plot_fn = prefix + DEFAULT_KNEE_PLOT_FN
     summary_fn = prefix + DEFAULT_BC_STAT_FN
 
-    if kit not in ['3v2', '3v3', '5v3']:
+    if kit not in ['3v2', '3v3', '5v2', '5v3']:
         helper.err_msg("Error: Invalid value of --kit-version (" + kit + "), please choose from 3v3 or 3v2 or 5v3") 
-        sys.exit()
+        sys.exit()  
 
     if full_bc_whitelist:
         helper.warning_msg(textwrap.dedent(
             f'You are using {os.path.basename(full_bc_whitelist)} as the full barcode '\
             'whitelist. Note that the barcodes not listed in the file will never be found.'))
     else:
         if kit == '3v3':
-            full_bc_whitelist = DEFAULT_GRB_WHITELIST_V3
-        elif kit == '3v2' or kit == '5v3':
+            full_bc_whitelist = DEFAULT_GRB_WHITELIST_3V3
+        elif kit == '3v2' or kit == '5v2':
             full_bc_whitelist = DEFAULT_GRB_WHITELIST_V2
+        elif kit == '5v3':
+            full_bc_whitelist = DEFAULT_GRB_WHITELIST_5V3
 
     # Read from args
     if not args:
@@ -735,7 +737,7 @@ def main(argv=None):
         logger.info(helper.warning_msg(
             f"NOTE: The `{out_fastq_fn}` exists and has NOT been updated.", printit = False))
 
-        if os.path.getmtime(out_fastq_fn) < os.path.getmtime(out_whitelist_fn):
+        if  os.path.exists(out_fastq_fn) and os.path.getmtime(out_fastq_fn) < os.path.getmtime(out_whitelist_fn):
             logger.info(helper.warning_msg(
             f"Warning: the existing `{out_fastq_fn}` is older than the upstream output {out_whitelist_fn}."
             f"If it needs to be re-generated. Please remove/rename the existing `{out_fastq_fn}` and re-run BLAZE "

setup.py

@@ -13,7 +13,7 @@
     test_suite='test',
     long_description=long_description,
     long_description_content_type='text/markdown',
-    package_data={'blaze': ['10X_bc/3M-february-2018.zip', '10X_bc/737K-august-2016.txt']},
+    package_data={'blaze': ['10X_bc/3M-february-2018.zip', '10X_bc/737K-august-2016.txt', '10X_bc/3M-5pgex-jan-2023.zip']},
     url="https://github.com/shimlab/BLAZE",
     install_requires=["fast-edit-distance==1.2.1", 
                     'matplotlib', 

test/run_test.sh

@@ -1,3 +1,6 @@
 # run the following command to test the above commands
 mkdir test_out
 blaze --expect-cells=500 --threads=12 --output-prefix test_out/test_ data/
+
+
+blaze --expect-cells=10 --threads=1 --full-bc-whitelist /home/youyupei/github_repo/shimlab/BLAZE/blaze/10X_bc/3M-5pgex-jan-2023.txt  --kit-version 5v3 --overwrite  --output-prefix  test_  test02.fastq.gzls