updated VEP pick csq criteria

sigven · Dec 15, 2023 · c809907 · c809907
1 parent f2f8e12
commit c809907
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Showing 3 changed files with 12 additions and 9 deletions.
diff --git a/pcgr/arg_checker.py b/pcgr/arg_checker.py
@@ -187,16 +187,19 @@ def check_args(arg_dict):
     # Check that VEP pick criteria is formatted correctly
     if not arg_dict['vep_pick_order'] is None:
         values = str(arg_dict['vep_pick_order']).split(',')
-        permitted_sources = ['canonical', 'appris', 'tsl', 'biotype', 'ccds', 'rank', 'length', 'mane_select','mane_plus_clinical']
+        permitted_sources = pcgr_vars.VEP_PICK_CRITERIA
         num_permitted_sources = 0
         for v in values:
             if v in permitted_sources:
                 num_permitted_sources += 1
 
-        if num_permitted_sources != 9:
-            err_msg = (f"'--vep_pick_order' = {arg_dict['vep_pick_order']} is formatted incorrectly, should be "
-                "a comma-separated string of the following values: mane_select,mane_plus_clinical,canonical,appris,tsl,biotype,ccds,rank,length")
+        if num_permitted_sources != len(pcgr_vars.VEP_PICK_CRITERIA):
+            err_msg = (
+                f"Option '--vep_pick_order' = {str(arg_dict['vep_pick_order'])} is formatted incorrectly, should be " 
+                f"a comma-separated string of the following values: '{' '.join(pcgr_vars.VEP_PICK_CRITERIA)}'"
+            )
             error_message(err_msg, logger)
+
     return
 
 
@@ -513,7 +516,7 @@ def check_args_cpsr(arg_dict):
             if v in permitted_sources:
                 num_permitted_sources += 1
 
-        if num_permitted_sources != 8:
+        if num_permitted_sources != len(pcgr_vars.VEP_PICK_CRITERIA):
             err_msg = (
                 f"Option '--vep_pick_order' = {str(arg_dict['vep_pick_order'])} is formatted incorrectly, should be " 
                 f"a comma-separated string of the following values: '{' '.join(pcgr_vars.VEP_PICK_CRITERIA)}'"

diff --git a/pcgr/cpsr.py b/pcgr/cpsr.py
@@ -44,9 +44,9 @@ def get_args():
     optional_other.add_argument('--version', action='version', version=str(utils.get_cpsr_version()))
     optional_other.add_argument('--no_reporting',action="store_true",help="Run functional variant annotation on VCF through VEP/vcfanno, omit classification/report generation (STEP 4), default: %(default)s")
     optional_other.add_argument('--retained_info_tags', dest ='retained_info_tags', default='None', help='Comma-separated string of VCF INFO tags from query VCF that should be kept in CPSR output TSV')
-    optional_other.add_argument('--report_theme',choices = ['default','cerulean','journal','flatly','readable','spacelab','united','cosmo','lumen','paper','sandstone','simplex','yeti'], default = 'default', help='Visual report theme (rmarkdown),  default: %(default)s' )
-    optional_other.add_argument('--report_nonfloating_toc', action='store_true', help='Do not float the table of contents (TOC) in output HTML report, default: %(default)s')
-    optional_other.add_argument('--report_table_display', choices = ['full','light'], default='light', help="Set the level of detail/comprehensiveness in interactive datables of HTML report, very comprehensive (option 'full') or slim/focused ('light'), default: %(default)s")
+    #optional_other.add_argument('--report_theme',choices = ['default','cerulean','journal','flatly','readable','spacelab','united','cosmo','lumen','paper','sandstone','simplex','yeti'], default = 'default', help='Visual report theme (rmarkdown),  default: %(default)s' )
+    #optional_other.add_argument('--report_nonfloating_toc', action='store_true', help='Do not float the table of contents (TOC) in output HTML report, default: %(default)s')
+    #optional_other.add_argument('--report_table_display', choices = ['full','light'], default='light', help="Set the level of detail/comprehensiveness in interactive datables of HTML report, very comprehensive (option 'full') or slim/focused ('light'), default: %(default)s")
     optional_other.add_argument('--ignore_noncoding', action='store_true',dest='ignore_noncoding',default=False,help='Ignore non-coding (i.e. non protein-altering) variants in report, default: %(default)s')
     optional_other.add_argument("--debug", action="store_true", help="Print full commands to log")
     optional_other.add_argument("--pcgrr_conda", default="pcgrr", help="pcgrr conda env name (default: %(default)s)")

diff --git a/pcgr/pcgr_vars.py b/pcgr/pcgr_vars.py
@@ -24,7 +24,7 @@
 VEP_MAX_FORKS = 8
 VEP_MIN_BUFFER_SIZE = 50
 VEP_MAX_BUFFER_SIZE = 30000
-VEP_PICK_CRITERIA = ['mane','canonical','appris','tsl','biotype','ccds','rank','length']
+VEP_PICK_CRITERIA = ['mane_select','mane_plus_clinical','canonical','appris','tsl','biotype','ccds','rank','length']
 
 tsites = {
     0: 'Any',