fix YAML grouping and gene grouped counts

ablab · Apr 16, 2024 · ff38421 · ff38421
1 parent d6b4bfb
commit ff38421
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/src/dataset_processor.py b/src/dataset_processor.py
@@ -323,8 +323,9 @@ def __init__(self, args, sample, read_groups, gffutils_db=None, chr_id=None, gzi
 
         if self.args.read_group and self.args.genedb:
             self.gene_grouped_counter = create_gene_counter(sample.out_gene_grouped_counts_tsv,
-                                                            self.args.gene_quantification, self.read_groups,
-                                                            self.gene_set)
+                                                            self.args.gene_quantification,
+                                                            self.gene_set,
+                                                            self.read_groups)
             self.transcript_grouped_counter = create_transcript_counter(sample.out_transcript_grouped_counts_tsv,
                                                                         self.args.transcript_quantification,
                                                                         self.transcript_set,

diff --git a/src/input_data_storage.py b/src/input_data_storage.py
@@ -246,7 +246,7 @@ def get_samples_from_yaml(self, yaml_file_path):
                     if names:
                         readable_name = sample['labels'][f]
                     else:
-                        readable_name = os.path.splitext(os.path.basename(fname[0]))[0]
+                        readable_name = os.path.splitext(os.path.basename(fname))[0]
                     if fname in readable_names_dict[current_sample_name]:
                         logger.critical("File %s is used multiple times in a single experiment, which is not allowed" % fname)
                         exit(-2)