remove keep raw option.

bigbio · Sep 4, 2023 · 29947dd · 29947dd
1 parent 975a2a7
commit 29947dd
Show file tree

Hide file tree

Showing 2 changed files with 15 additions and 33 deletions.
diff --git a/sdrf_pipelines/openms/openms.py b/sdrf_pipelines/openms/openms.py
@@ -23,20 +23,16 @@ class FileToColumnEntries:
     file2technical_rep = {}
 
 
-def get_openms_file_name(raw, keep_raw: bool, extension_convert: str = None):
+def get_openms_file_name(raw, extension_convert: str = None):
     """
-    Convert file name for OpenMS, for if keep raw is set the same filename will be returned.
-    - file.raw -> file.raw  (keep_raw=True)
-    - file.raw -> file.mzML  (keep_raw=False)
-    However, if extension_convert is set, the extension will be converted to the specified format.
+    Convert file name for OpenMS. If extension_convert is set, the extension will be converted to the specified format.
     - file.raw -> file.mzML  (extension_convert=raw:mzML)
     - file.mzML -> file.mzML  (extension_convert=mzML:mzML)
     - file.mzML -> file.mzml  (extension_convert=mzML:mzml)
     - file.mzml -> file.mzML  (extension_convert=mzml:mzML)
     - file.d -> file.mzML  (extension_convert=d:mzML)
     - file.d -> file.d  (extension_convert=d:d)
     :param raw: raw file name
-    :param keep_raw: keep raw file name
     :param extension_convert: convert extension to specified format
     :return: converted file name
     """
@@ -56,9 +52,6 @@ def get_openms_file_name(raw, keep_raw: bool, extension_convert: str = None):
             )
         out = ext[0] + "." + new_extension
         return out
-    if not keep_raw:
-        ext = os.path.splitext(raw)
-        out = ext[0] + ".mzML"
     else:
         out = raw
 
@@ -214,7 +207,6 @@ def openms_ify_mods(self, sdrf_mods):
     def openms_convert(
         self,
         sdrf_file: str = None,
-        keep_raw: bool = False,
         one_table: bool = False,
         legacy: bool = False,
         verbose: bool = False,
@@ -429,7 +421,6 @@ def openms_convert(
                     source_name2n_reps,
                     f2c.file2combined_factors,
                     f2c.file2label,
-                    keep_raw,
                     extension_convert,
                     f2c.file2fraction,
                 )
@@ -441,7 +432,6 @@ def openms_convert(
                     source_name_list,
                     source_name2n_reps,
                     f2c.file2label,
-                    keep_raw,
                     extension_convert,
                     f2c.file2fraction,
                     f2c.file2combined_factors,
@@ -466,7 +456,6 @@ def openms_convert(
                         source_name2n_reps,
                         f2c.file2combined_factors,
                         f2c.file2label,
-                        keep_raw,
                         extension_convert,
                         f2c.file2fraction,
                     )
@@ -478,7 +467,6 @@ def openms_convert(
                         source_name_list,
                         source_name2n_reps,
                         f2c.file2label,
-                        keep_raw,
                         extension_convert,
                         f2c.file2fraction,
                         f2c.file2combined_factors,
@@ -530,7 +518,6 @@ def writeTwoTableExperimentalDesign(
         source_name_list,
         source_name2n_reps,
         file2label,
-        keep_raw,
         extension_convert,
         file2fraction,
         file2combined_factors,
@@ -628,7 +615,7 @@ def writeTwoTableExperimentalDesign(
                 else:
                     label = str(self.itraq4plex[label[label_index[raw]].lower()])
                 label_index[raw] = label_index[raw] + 1
-            out = get_openms_file_name(raw, keep_raw, extension_convert)
+            out = get_openms_file_name(raw, extension_convert)
 
             f.write(
                 str(Fraction_group[raw])
@@ -718,7 +705,6 @@ def writeOneTableExperimentalDesign(
         source_name2n_reps,
         file2combined_factors,
         file2label,
-        keep_raw,
         extension_convert,
         file2fraction,
     ):
@@ -884,7 +870,7 @@ def writeOneTableExperimentalDesign(
                     label = str(self.itraq4plex[label[label_index[raw]].lower()])
                 label_index[raw] = label_index[raw] + 1
 
-            out = get_openms_file_name(raw, keep_raw, extension_convert)
+            out = get_openms_file_name(raw, extension_convert)
 
             if "MSstats_Mixture" in open_ms_experimental_design_header:
                 if raw not in mixture_raw_tag.keys():

diff --git a/sdrf_pipelines/parse_sdrf.py b/sdrf_pipelines/parse_sdrf.py
@@ -33,23 +33,21 @@ def cli():
 
 @click.command("convert-openms", short_help="convert sdrf to openms file output")
 @click.option("--sdrf", "-s", help="SDRF file")
-@click.option("--raw", "-r", help="Keep filenames in experimental design output as raw.", is_flag=True)
-@click.option(
-    "--legacy/--modern", "-l/-m", default=False, help="legacy=Create artificial sample column not needed in OpenMS 2.6."
-)
-@click.option("--onetable/--twotables", "-t1/-t2", default=False, help="Create one-table or two-tables format.")
-@click.option("--verbose/--quiet", "-v/-q", default=False, help="Output debug information.")
-@click.option("--conditionsfromcolumns", "-c", help="Create conditions from provided (e.g., factor) columns.")
-@click.option(
-    "--extension_convert",
-    "-e",
-    help="convert extensions of files from one type to other 'raw:mzML,mzml:MZML,mzML:mzML,d:d'",
+@click.option("--legacy/--modern", "-l/-m", default=False,
+              help="legacy=Create artificial sample column not needed in OpenMS 2.6.")
+@click.option("--onetable/--twotables", "-t1/-t2",
+              help="Create one-table or two-tables format.", default=False )
+@click.option("--verbose/--quiet", "-v/-q",
+              help="Output debug information.", default=False)
+@click.option("--conditionsfromcolumns", "-c",
+              help="Create conditions from provided (e.g., factor) columns.")
+@click.option("--extension_convert","-e",
+              help="convert extensions of files from one type to other 'raw:mzML,mzml:MZML,mzML:mzML,d:d'",
 )
 @click.pass_context
 def openms_from_sdrf(
     ctx,
     sdrf: str,
-    raw: bool,
     onetable: bool,
     legacy: bool,
     verbose: bool,
@@ -58,10 +56,8 @@ def openms_from_sdrf(
 ):
     if sdrf is None:
         help()
-    if extension_convert is not None and raw:
-        logging.info("The raw option (keeping file names) is overwritten by the extension_convert option.")
     try:
-        OpenMS().openms_convert(sdrf, raw, onetable, legacy, verbose, conditionsfromcolumns, extension_convert)
+        OpenMS().openms_convert(sdrf, onetable, legacy, verbose, conditionsfromcolumns, extension_convert)
     except Exception as ex:
         print("Error: " + str(ex))