varvamp 0.8__py3-none-any.whl → 0.8.2__py3-none-any.whl

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/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/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/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.dist-info → varvamp-0.8.2.dist-info}/METADATA

@@ -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.dist-info → varvamp-0.8.2.dist-info}/RECORD

@@ -1,19 +1,19 @@
-varvamp/__init__.py,sha256=OVljE8H3MzOgM-oEcwY1qgcBuf6kPeA00EPpUCrQC9g,105
+varvamp/__init__.py,sha256=6ftSwxs5TY7JG0KbwIz62AUA-2eblnr5J56Lkj-Otgg,107
 varvamp/__main__.py,sha256=9R3mbX2_Q5LByPx8WLoTbvZ-G2dbRSMpDlgze0Wm5Fc,98
-varvamp/command.py,sha256=gbJi5qifpEekXF9HnwGWftF9dGJG6DLGirrBDf1RANQ,16232
+varvamp/command.py,sha256=erWMFwJpZ4OLBKmBtrcHuUkVZfvyranJq__vJMd2m4Y,16232
 varvamp/scripts/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-varvamp/scripts/alignment.py,sha256=uJbsjCMEigYNY36pw7DD5-zp0u05UaYrWKL0rarOA8Y,6868
+varvamp/scripts/alignment.py,sha256=jNQEtjmohSVtBlzP5wUVzZzVZl012waWGxfe9n9ArzY,6974
 varvamp/scripts/config.py,sha256=CSk2-OBTDyJoNDpHTDP8f7yHbZTF9QE-PQUULJMplZE,2290
 varvamp/scripts/consensus.py,sha256=dp8WXQSB2of1Fi3bPtJYX4bHhGQmEvTUAO1pQ1fG-wQ,3374
 varvamp/scripts/logging.py,sha256=l8tEpz6cnz6MjV3TwW0ofozwza-9BnReyuzJmrnc2MI,14427
-varvamp/scripts/param_estimation.py,sha256=GGclU0RdikYRlx8wCLsl43y24xbDwBz_-35lLL7kNLE,3643
+varvamp/scripts/param_estimation.py,sha256=nOZpDtf480CQ_ckTxdIhl53qmY3kkKRhiOcSTRarMag,3690
 varvamp/scripts/primers.py,sha256=LzNnYJhgdxZJMHQe-GfKZnR8vIWE77fPcijtfErxo-U,12939
 varvamp/scripts/qpcr.py,sha256=-EwYXnR0dmsS_WkCVLIlr2pCXmbifOUHwG8gJCUS2FQ,11623
 varvamp/scripts/regions.py,sha256=vLNOVicod5tup-svQYOMIooaqkkiM2gIGHBscDu3oUU,3273
 varvamp/scripts/reporting.py,sha256=-M0BsB-QKF4x8YGljPaJAvKKniPRWlz7I4_zOHxiyBA,19760
 varvamp/scripts/scheme.py,sha256=nkkcf5rFXAbtuidWBTMef6DM5ZZXMh9bpZ0vldhs7IM,15719
-varvamp-0.8.dist-info/METADATA,sha256=Dl5E3MibwjrccWD1oOcH_PzovT5SdgnuVbdnoYW68s0,4351
-varvamp-0.8.dist-info/WHEEL,sha256=pkctZYzUS4AYVn6dJ-7367OJZivF2e8RA9b_ZBjif18,92
-varvamp-0.8.dist-info/entry_points.txt,sha256=puzW-basyBexZT4JVRUfUEqobvFmEyfqRQaqFjp7rB0,49
-varvamp-0.8.dist-info/top_level.txt,sha256=11oVwE3SBUB9aTmvpvEDru95Tc5GZqQikzzFjw2eVGc,8
-varvamp-0.8.dist-info/RECORD,,
+varvamp-0.8.2.dist-info/METADATA,sha256=j7-hHm1heJEdN3Y_F8gixD0hqI8pRPaFU1KkwXMcDWI,4353
+varvamp-0.8.2.dist-info/WHEEL,sha256=pkctZYzUS4AYVn6dJ-7367OJZivF2e8RA9b_ZBjif18,92
+varvamp-0.8.2.dist-info/entry_points.txt,sha256=puzW-basyBexZT4JVRUfUEqobvFmEyfqRQaqFjp7rB0,49
+varvamp-0.8.2.dist-info/top_level.txt,sha256=11oVwE3SBUB9aTmvpvEDru95Tc5GZqQikzzFjw2eVGc,8
+varvamp-0.8.2.dist-info/RECORD,,