update cellrange multi to handle both fb and ch

mskcc · Dec 30, 2024 · 724afce · 724afce
1 parent 0c91752
commit 724afce
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Showing 2 changed files with 9 additions and 10 deletions.
diff --git a/scripts/cellranger_multi.py b/scripts/cellranger_multi.py
@@ -185,7 +185,7 @@ def update_fastq_location(self, sub_sample_name, destination):
 # read ch file from shared drive and generate config/ch file per sample and return sample to sub sample info also
 # default all hash tag are totalseq B from biolegend
 def ch_file_generation(project_id, sample_name):
-    in_file_location = DRIVE_LOCATION + project_id + "/" + os.listdir(DRIVE_LOCATION + project_id)[0]
+    in_file_location = glob.glob("{}{}/*cell_hash.xlsx".format(DRIVE_LOCATION, project_id))[0]
     with open(in_file_location, "rb") as f:
         df = pd.read_excel(f, engine="openpyxl")
     line_number = df[df[df.columns[0]] == "Your Submission:"].index.values
@@ -219,7 +219,7 @@ def ch_file_generation(project_id, sample_name):
 
 # create fb template from user submitted file
 def fb_file_generation(project_ID):
-    file_path = DRIVE_LOCATION + project_ID + "/" + os.listdir(DRIVE_LOCATION + project_ID)[0]
+    file_path = glob.glob("{}{}/*feature_barcoding.xlsx".format(DRIVE_LOCATION, project_ID))[0]
     with open(file_path, "rb") as f:
         df = pd.read_excel(f, engine="openpyxl")
     line_number = df[df[df.columns[0]] == "Your Submission:"].index.values
@@ -258,8 +258,7 @@ def gather_config_info(sample_dict, genome, IGO_ID):
 
     # if feature barcoding invovled, add feature list file path and create fb template
     if "fb" in sample_dict.keys():
-        if "ch" not in sample_dict.keys():
-            fb_file_generation(project_ID)
+        fb_file_generation(project_ID)
         config.features = CONFIG_AREA + "Project_{}/Project_{}_fb.csv".format(project_ID, project_ID)
 
     # if cell hashing invovled, add cmo-set file path and get sample info from file, id as sample name and name as hashtag name

diff --git a/stats_by_project_dag.py b/stats_by_project_dag.py
@@ -52,14 +52,14 @@ def run_stats(ds, **kwargs):
                 file_type = scripts.cellranger_multi.check_file_type(file_path)
                 if file_type == "ch":
                     ch = True
-                    cmd = "mv {} {}/{}_cell_hash.xlsx".format(file_path, file_prefix, project_id)
-                    print(cmd)
-                    subprocess.run(cmd, shell=True)
+                    ch_file_name = "{}/{}_cell_hash.xlsx".format(file_prefix, project_id)
+                    os.rename(file_path, ch_file_name)
+                    print(f"File renamed from {file_path} to {ch_file_name}")
                 elif file_type == "fb":
                     fb = True
-                    cmd = "mv {} {}/{}_feature_barcoding.xlsx".format(file_path, file_prefix, project_id)
-                    print(cmd)
-                    subprocess.run(cmd, shell=True)
+                    fb_file_name = "{}/{}_feature_barcoding.xlsx".format(file_prefix, project_id)
+                    os.rename(file_path, fb_file_name)
+                    print(f"File renamed from {file_path} to {fb_file_name}")
 
             os.chdir(scripts.cellranger_multi.STATS_AREA)
             # gather sample set info from LIMS for each sample