celescope 2.2.0.dev0__tar.gz → 2.2.0.dev1__tar.gz

{celescope-2.2.0.dev0/celescope.egg-info → celescope-2.2.0.dev1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: celescope
-Version: 2.2.0.dev0
+Version: 2.2.0.dev1
 Summary: Single Cell Analysis Pipelines
 Home-page: https://github.com/singleron-RD/CeleScope
 Author: zhouyiqi

{celescope-2.2.0.dev0 → celescope-2.2.0.dev1}/celescope/__init__.py

@@ -1,6 +1,6 @@
 import os
 
-__VERSION__ = "2.2.0dev"
+__VERSION__ = "2.2.0dev1"
 __version__ = __VERSION__
 
 ASSAY_LIST = [

{celescope-2.2.0.dev0 → celescope-2.2.0.dev1}/celescope/pathseq/analysis_pathseq.py

@@ -12,7 +12,8 @@ def get_opts_analysis_pathseq(parser, sub_program):
         parser.add_argument(
             "--umi_matrix_file", help="UMI matrix tsv file", required=True
         )
-        parser.add_argument("--match_dir", help=HELP_DICT["match_dir"], required=True)
+        parser.add_argument("--match_dir", help=HELP_DICT["match_dir"])
+        parser.add_argument("--tsne_coord_file")
         s_common(parser)
 
 
@@ -25,8 +26,12 @@ class Analysis_pathseq(Step):
     def __init__(self, args, display_title):
         super().__init__(args, display_title)
 
-        match_dict = parse_match_dir(self.args.match_dir)
-        self.df_tsne = read_tsne(match_dict["tsne_coord"])
+        if args.match_dir:
+            match_dict = parse_match_dir(self.args.match_dir)
+            tsne_file = match_dict["tsne_coord"]
+        else:
+            tsne_file = args.tsne_coord_file
+        self.df_tsne = read_tsne(tsne_file)
         self.df_umi = pd.read_csv(self.args.umi_matrix_file, sep="\t", index_col=0).T
 
     def add_dropdown_plot(self):

{celescope-2.2.0.dev0 → celescope-2.2.0.dev1}/celescope/pathseq/count_pathseq.py

@@ -15,8 +15,11 @@ class Count_pathseq(Step):
     def __init__(self, args, display_title=None):
         Step.__init__(self, args, display_title=display_title)
         # match
-        self.match_dict = utils.parse_match_dir(args.match_dir)
-        self.match_barcode = self.match_dict["match_barcode"]
+        if args.match_dir:
+            self.match_dict = utils.parse_match_dir(args.match_dir)
+            self.match_barcode = self.match_dict["match_barcode"]
+        else:
+            self.match_barcode, _ = utils.get_barcode_from_matrix_dir(args.matrix_dir)
 
         # out
         self.raw_matrix_file = f"{self.outdir}/{self.sample}_raw_UMI_matrix.tsv.gz"
@@ -157,6 +160,7 @@ def get_opts_count_pathseq(parser, sub_program):
             "--pathseq_score_file", help="pathseq score file", required=True
         )
         parser.add_argument("--unmap_bam_file", help="unmap bam file", required=True)
-        parser.add_argument("--match_dir", help=HELP_DICT["match_dir"], required=True)
+        parser.add_argument("--match_dir", help=HELP_DICT["match_dir"])
+        parser.add_argument("--matrix_dir")
         s_common(parser)
     return parser

{celescope-2.2.0.dev0 → celescope-2.2.0.dev1}/celescope/tools/utils.py

@@ -281,7 +281,7 @@ def get_barcode_from_matrix_dir(matrix_dir):
     """
     Returns:
         match_barcode: list
-        no_match_barcode: int
+        n_match_barcode: int
     """
 
     match_barcode_file = get_matrix_file_path(matrix_dir, BARCODE_FILE_NAME)

{celescope-2.2.0.dev0 → celescope-2.2.0.dev1/celescope.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: celescope
-Version: 2.2.0.dev0
+Version: 2.2.0.dev1
 Summary: Single Cell Analysis Pipelines
 Home-page: https://github.com/singleron-RD/CeleScope
 Author: zhouyiqi