Added --force-samples argument. Added text to model file exception

pgpipe/model.py

@@ -100,7 +100,7 @@ def create_ind_file (self, file_ext = '', file_path = '', overwrite = False):
         if not overwrite:
             # Check if the file already exists
             if os.path.isfile(ind_filename):
-                raise IOError('Individuals file exists.')
+                raise IOError('Individuals file exists. Use --overwrite to ignore')
 
         # Create the population file
         ind_file = open(ind_filename, 'w')

pgpipe/vcf_filter.py

@@ -183,6 +183,14 @@
         Argument used to include positions with the specified filter flag.
     **--filter-exclude-filtered** *<filter_flag>*
         Argument used to exclude positions with the specified filter flag.
+
+    #############################
+    Other Command-line Arguments
+    #############################
+    **--force-samples**
+        Argument used to ignore the error rasied when a sample that does not exist
+        within the input VCF.
+
 '''
 
 import os
@@ -265,8 +273,9 @@ def metavar_list (var_list):
 
     vcf_parser.add_argument('--out-format', metavar = metavar_list(out_format_list), help = 'Defines the desired output format', type = str, choices = out_format_list, default = out_format_default)
 
-    # General arguments.
+    # General arguments
     vcf_parser.add_argument('--overwrite', help = "Overwrite previous output", action = 'store_true')
+    vcf_parser.add_argument('--force-samples', help = "Ignore the error rasied when a sample that does not exist", action = 'store_true')
 
     # Galaxy Option to pipe log to stdout
     vcf_parser.add_argument('--log-stdout', help = argparse.SUPPRESS, action = 'store_true')
@@ -654,6 +663,10 @@ def run (**kwargs):
         if vcf_args.filter_mac_max != None:
             bcftools_call_args.extend(['--max-ac', vcf_args.filter_mac_max])
 
+    # Check if samples should be forced
+    if vcf_args.force_samples:
+        bcftools_call_args.append('--force-samples')
+
     # List to store expression for BCFtools include expression functionality
     bcftools_expressions = []