deleting the suffix for the outputs

CNIC-Proteomics · Nov 13, 2024 · 9763504 · 9763504
1 parent 6f6464d
commit 9763504
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Showing 2 changed files with 18 additions and 7 deletions.
diff --git a/add_scanid.py b/add_scanid.py
@@ -54,10 +54,17 @@ def main(args):
     # get the base name of the input file
     # construct output file path with "_XXX" appended to the filename
     # log files
-    outdir = args.outdir if args.outdir else os.path.dirname(ifile)
-    basename = os.path.splitext(os.path.basename(ifile))[0]
-    extension = os.path.splitext(os.path.basename(ifile))[1]
-    ofile = os.path.join(outdir, f"{basename}_ScanID{extension}")
+
+    # outdir = args.outdir if args.outdir else os.path.dirname(ifile)
+    # basename = os.path.splitext(os.path.basename(ifile))[0]
+    # extension = os.path.splitext(os.path.basename(ifile))[1]
+    # ofile = os.path.join(outdir, f"{basename}_ScanID{extension}")
+
+    outdir = args.outdir if args.outdir else os.path.join(os.path.dirname(ifile), script_name.lower())
+    os.makedirs(outdir, exist_ok=False)
+    basename = os.path.basename(ifile)
+    ofile = os.path.join(outdir, basename)
+
     # get the list of column names that compose the ScanID
     ids = re.split(r'\s*,\s*', args.ids)
 

diff --git a/mz_extractor.py b/mz_extractor.py
@@ -200,10 +200,12 @@ def print_by_experiment(df, outdir):
     # create workspace
     if not os.path.exists(outdir):
         os.makedirs(outdir, exist_ok=False)
-    # remove obsolete file
+    # create temporal file
     name = os.path.splitext(os.path.basename(exp))[0]
     ext = os.path.splitext(os.path.basename(exp))[-1] or '.tsv'
-    ofile = f"{outdir}/{name}_quant{ext}.tmp"
+    ofile = f"{outdir}/{name}{ext}.tmp"
+    # basename = os.path.basename(exp)
+    # ofile = os.path.join(outdir, f"{basename}.tmp")
     if os.path.isfile(ofile):
         os.remove(ofile)
     # print
@@ -253,10 +255,12 @@ def main(args):
 
 
     logging.info("print the ID files by experiments")
+    # get the outputdir. The filename by default
+    outdir = args.outdir if args.outdir else os.path.join(os.path.dirname(ifile), script_name.lower())
     with concurrent.futures.ProcessPoolExecutor(max_workers=args.n_workers) as executor:        
         tmpfiles = executor.map( print_by_experiment,
                                 list(ddf.groupby("Spectrum_File")),
-                                itertools.repeat(args.outdir) )
+                                itertools.repeat(outdir) )
     [common.rename_tmpfile(f) for f in list(tmpfiles)] # rename tmp file deleting before the original file 
     # # begin: for debugging in Spyder
     # tmpfile = print_by_experiment(list(ddf.groupby("Spectrum_File"))[0], args.outdir)