fix: take arg string in the blaze() function

shimlab · Dec 17, 2024 · cdb77d2 · cdb77d2
1 parent ad625d4
commit cdb77d2
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Showing 2 changed files with 7 additions and 5 deletions.
diff --git a/blaze/main.py b/blaze/main.py
@@ -328,9 +328,9 @@ def print_logo(args):
                 {BLAZE_LOGO}
         '''))
 
-def main():
+def main(args_string=None):
     # Start running: Welcome logo
-    args = parse_arg()
+    args = parse_arg(args_string)
     print_logo(args)
 
     # TMP: print all the arguments in args

diff --git a/blaze/parser.py b/blaze/parser.py
@@ -16,7 +16,7 @@
 logger = logging.getLogger(__name__)
 logger.setLevel(logging.DEBUG)
 
-def parse_arg():
+def parse_arg(arg_string=None):
     parser = argparse.ArgumentParser(
     description=textwrap.dedent(helper.bold_text(
     '''BLAZE2 is a tool for demultiplexing 10X single cell long-read RNA-seq data. It takes fastq files as 
@@ -127,8 +127,10 @@ def get_files_from_dir(fastq_dir):
     ###############################
     ####### checking the argument:
     ###############################
-
-    args = parser.parse_args()
+    if arg_string is None:
+        args = parser.parse_args()
+    else:
+        args = parser.parse_args(arg_string.split())
 
     # config the output filenames
     args.output_fastq = args.output_prefix + args.output_fastq