varvamp 0.8__tar.gz → 0.8.2__tar.gz

{varvamp-0.8 → varvamp-0.8.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: varvamp
-Version: 0.8
+Version: 0.8.2
 Summary: Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses
 Home-page: https://github.com/jonas-fuchs/varVAMP
 Author: Dr. Jonas Fuchs

{varvamp-0.8 → varvamp-0.8.2}/varvamp/__init__.py

@@ -1,3 +1,3 @@
 """Tool to design amplicons for highly variable virusgenomes"""
 _program = "varvamp"
-__version__ = "0.8"
+__version__ = "0.8.2"

{varvamp-0.8 → varvamp-0.8.2}/varvamp/command.py

@@ -163,7 +163,7 @@ def shared_workflow(args, log_file):
     if args.mode == "qpcr" and args.n_ambig >= 1 and args.pn_ambig is None:
         args.pn_ambig = args.n_ambig - 1
         with open(log_file, "a") as f:
-            print(f"Automatic parameter selection set -pn {args.pn_ambig}.", file=f)
+            print(f"Automatic parameter selection set -pa {args.pn_ambig}.", file=f)
 
     # check arguments
     logging.raise_arg_errors(args, log_file)

{varvamp-0.8 → varvamp-0.8.2}/varvamp/scripts/alignment.py

@@ -215,9 +215,12 @@ def process_alignment(preprocessed_alignment, threshold):
     if unique_gaps:
         gap_dic = create_gap_dictionary(unique_gaps, all_gaps)
         gaps_to_mask = find_gaps_to_mask(gap_dic, gap_cutoff)
-        alignment_cleaned = clean_gaps(
-            preprocessed_alignment, gaps_to_mask
-        )
+        if gaps_to_mask:
+            alignment_cleaned = clean_gaps(
+                preprocessed_alignment, gaps_to_mask
+            )
+        else:
+            alignment_cleaned = preprocessed_alignment
     else:
         gaps_to_mask = []
         alignment_cleaned = preprocessed_alignment

{varvamp-0.8 → varvamp-0.8.2}/varvamp/scripts/param_estimation.py

@@ -38,11 +38,11 @@ def calculate_distances(all_freqs, threshold):
     previous_dis = 0
     all_dis = []
 
-    for freq in all_freqs:
+    for idx, freq in enumerate(all_freqs):
         if freq < threshold:
             current_dis = 0
         current_dis += 1
-        if current_dis <= previous_dis:
+        if current_dis <= previous_dis or idx == len(all_freqs)-1:
             all_dis.append(previous_dis)
 
         previous_dis = current_dis
@@ -85,7 +85,7 @@ def get_parameters(preprocessed_alignment, args, log_file):
                 [distances[x] for x in range(0, len(distances)) if sum(distances[x:x+args.n_ambig+1]) >= config.PRIMER_SIZES[0]]
             )
             # calculate coverage
-            coverage = covered_pos/len(preprocessed_alignment[0][1])
+            coverage = (covered_pos+1)/len(preprocessed_alignment[0][1])
             # change the non fixed param if threshold has not been reached
             if coverage >= 0.5:
                 # write each iteration to log

{varvamp-0.8 → varvamp-0.8.2}/varvamp.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: varvamp
-Version: 0.8
+Version: 0.8.2
 Summary: Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses
 Home-page: https://github.com/jonas-fuchs/varVAMP
 Author: Dr. Jonas Fuchs