varvamp 1.1.1__py3-none-any.whl → 1.1.2__py3-none-any.whl

varvamp/__init__.py

@@ -1,3 +1,3 @@
 """Tool to design amplicons for highly variable virusgenomes"""
 _program = "varvamp"
-__version__ = "1.1.1"
+__version__ = "1.1.2"

varvamp/command.py

@@ -180,8 +180,11 @@ def shared_workflow(args, log_file):
     # estimate threshold or number of ambiguous bases if args were not supplied
     if args.threshold is None or args.n_ambig is None:
         args.threshold, args.n_ambig = param_estimation.get_parameters(preprocessed_alignment, 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
+    if args.mode == "qpcr" and args.pn_ambig is None:
+        if args.n_ambig == 0:
+            args.pn_ambig = 0
+        if args.n_ambig > 0:
+            args.pn_ambig = args.n_ambig - 1
         with open(log_file, "a") as f:
             print(f"Automatic parameter selection set -pa {args.pn_ambig}.", file=f)
 

varvamp/scripts/logging.py

@@ -173,7 +173,7 @@ def raise_arg_errors(args, log_file):
     if args.mode == "qpcr":
         if args.pn_ambig < 0:
             raise_error(
-                "number of ambiguous characters in the qPCR probe cannot be 0.",
+                "number of ambiguous characters in the qPCR probe cannot be negative.",
                 log_file,
                 exit=True
             )
@@ -283,6 +283,7 @@ def confirm_config(args, log_file):
             "QPRIMER_DIFF",
             "QPROBE_TEMP_DIFF",
             "QPROBE_DISTANCE",
+            "END_OVERLAP",
             "QAMPLICON_LENGTH",
             "QAMPLICON_GC",
             "QAMPLICON_DEL_CUTOFF"
@@ -379,6 +380,7 @@ def confirm_config(args, log_file):
         ("max base penalty", config.PRIMER_MAX_BASE_PENALTY),
         ("primer permutation penalty", config.PRIMER_PERMUTATION_PENALTY),
         ("qpcr flanking primer difference", config.QPRIMER_DIFF),
+        ("probe and primer end overlap", config.END_OVERLAP),
         ("qpcr deletion size still considered for deltaG calculation", config.QAMPLICON_DEL_CUTOFF),
         ("maximum difference between primer and blast db", config.BLAST_MAX_DIFF),
         ("multiplier of the maximum length for non-specific amplicons", config.BLAST_SIZE_MULTI),

{varvamp-1.1.1.dist-info → varvamp-1.1.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: varvamp
-Version: 1.1.1
+Version: 1.1.2
 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-1.1.1.dist-info → varvamp-1.1.2.dist-info}/RECORD

@@ -1,21 +1,21 @@
-varvamp/__init__.py,sha256=uwHaZ8Uor-vHjXDetrw3COEIXmM2DwTl5iKzzuH5DtA,107
+varvamp/__init__.py,sha256=K5ccRm45N-jlwv4_LFmzwr4rl9NgmWICL5kNY_00-RE,107
 varvamp/__main__.py,sha256=9R3mbX2_Q5LByPx8WLoTbvZ-G2dbRSMpDlgze0Wm5Fc,98
-varvamp/command.py,sha256=Zz605uDIUyipibYT95P1fG0RtVyEF6yIYmpKezP-QXA,18445
+varvamp/command.py,sha256=rCP0k7wb2vbnlSKwTRkla4_pGQBl972EGmyWRBjfKXA,18516
 varvamp/scripts/__init__.py,sha256=DtRsgfnA60BvccKMuD-Ueo1UpxaeANUfIWxGi1xPcV0,46
 varvamp/scripts/alignment.py,sha256=w2I7BnaUt_rh1EaDQaU9Q_dmL_q019NtnaC8YMccOgM,7317
 varvamp/scripts/blast.py,sha256=029mOX07f6l_czDrj_OKH1KKnlfgjx2eZ7MNRykIkAI,9705
 varvamp/scripts/consensus.py,sha256=eU5eKU9iXyWeln2BW_LMPI8JiEq0_NXBI0jy4kMOvQg,3375
 varvamp/scripts/default_config.py,sha256=FkZUiIy8McyFXRzd8UTTTVRPbWNS8Oxmye3i-WsyDWw,3876
 varvamp/scripts/get_config.py,sha256=Kvg3YhttUbDeRxjKhfxLjI5JSKpPoiLSEYqcE6rT4Xk,2940
-varvamp/scripts/logging.py,sha256=u6Dvh3qNObedMiRw6HgiJoY1B0UDNEhloN8508-1HrY,20528
+varvamp/scripts/logging.py,sha256=ftOrySTkh5y0dEXQSDMJHMjA7Q9myJv9EhRcb6SmERc,20624
 varvamp/scripts/param_estimation.py,sha256=jpfmbjCFp23V07af3y1uO2dQZJiWLlyOBa11aMphkko,3694
 varvamp/scripts/primers.py,sha256=IEOoccW5OKK8d2a0ZQ1L1CICZIzOqKfeZp5e8iE717I,13428
 varvamp/scripts/qpcr.py,sha256=Oh1HUJ6QF3dvghS5LceUgZqC5UHNB1arOsxQVNa-WnY,14483
 varvamp/scripts/regions.py,sha256=VgYAlZmkC3rT946yhAdxATi-YT4oGcEwAPa0BkkfWIg,3239
 varvamp/scripts/reporting.py,sha256=CT_ZD9-73Di56zBHmaQ8Kr4VkWjqf8zgb0ohk8_8Puo,21338
 varvamp/scripts/scheme.py,sha256=rHeigj-tYyLJgB4w5F5tXZA-kkXkpDZ-kKpdE1Elonk,15229
-varvamp-1.1.1.dist-info/METADATA,sha256=be7ZIcJMmK9aE_wd3tprRYP0pJBgaHLg7fbIzKeSgtE,5149
-varvamp-1.1.1.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-varvamp-1.1.1.dist-info/entry_points.txt,sha256=puzW-basyBexZT4JVRUfUEqobvFmEyfqRQaqFjp7rB0,49
-varvamp-1.1.1.dist-info/top_level.txt,sha256=11oVwE3SBUB9aTmvpvEDru95Tc5GZqQikzzFjw2eVGc,8
-varvamp-1.1.1.dist-info/RECORD,,
+varvamp-1.1.2.dist-info/METADATA,sha256=FUi-1qMgSjFnwHZm-4RQbgHi4P46_DYUs7FfOS-B1xM,5149
+varvamp-1.1.2.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+varvamp-1.1.2.dist-info/entry_points.txt,sha256=puzW-basyBexZT4JVRUfUEqobvFmEyfqRQaqFjp7rB0,49
+varvamp-1.1.2.dist-info/top_level.txt,sha256=11oVwE3SBUB9aTmvpvEDru95Tc5GZqQikzzFjw2eVGc,8
+varvamp-1.1.2.dist-info/RECORD,,

{varvamp-1.1.1.dist-info → varvamp-1.1.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.42.0)
+Generator: bdist_wheel (0.43.0)
 Root-Is-Purelib: true
 Tag: py3-none-any