varvamp 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"
+__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/blast.py

@@ -58,7 +58,7 @@ def create_BLAST_query_qpcr(qpcr_scheme_candidates, data_dir):
     query_path = os.path.join(data_dir, "BLAST_query.fasta")
     with open(query_path, "w") as query:
         for amp in qpcr_scheme_candidates:
-            for primer_type in ["probe", "left", "right"]:
+            for primer_type in ["PROBE", "LEFT", "RIGHT"]:
                 name = f"{primer_type}_{qpcr_scheme_candidates[amp][primer_type][1]}_{qpcr_scheme_candidates[amp][primer_type][2]}"
                 if name in already_written:
                     continue
@@ -174,7 +174,7 @@ def predict_non_specific_amplicons_worker(amp, blast_df, max_length, mode):
         primers = [data[2], data[3]]
     elif mode == "qpcr":
         primers = []
-        for primer_type in ["probe", "left", "right"]:
+        for primer_type in ["PROBE", "LEFT", "RIGHT"]:
             primers.append(f"{primer_type}_{data[primer_type][1]}_{data[primer_type][2]}")
     # subset df for primers
     df_amp_primers = blast_df[blast_df["query"].isin(primers)]

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/scripts/primers.py

@@ -350,9 +350,9 @@ def create_primer_dictionary(primer_candidates, direction):
 
     for primer in primer_candidates:
         if direction == "+":
-            direction_name = "FW"
+            direction_name = "LEFT"
         elif direction == "-":
-            direction_name = "RV"
+            direction_name = "RIGHT"
         primer_name = f"{direction_name}_{primer_idx}"
         primer_dict[primer_name] = primer
         primer_idx += 1

varvamp/scripts/qpcr.py

@@ -82,7 +82,7 @@ def get_qpcr_probes(kmers, ambiguous_consensus, alignment_cleaned):
         # create probe dictionary
         if "+" in direction:
             if filter_probe_direction_dependent(kmer[0]):
-                probe_name = f"PROBE_{probe_idx}_FW"
+                probe_name = f"PROBE_{probe_idx}_LEFT"
                 three_prime_penalty = primers.calc_3_prime_penalty("+", per_base_mismatches)
                 probe_candidates[probe_name] = [kmer[0], kmer[1], kmer[2],
                                                 base_penalty + permutation_penalty + three_prime_penalty,
@@ -90,7 +90,7 @@ def get_qpcr_probes(kmers, ambiguous_consensus, alignment_cleaned):
                 probe_idx += 1
         if "-" in direction:
             if filter_probe_direction_dependent(primers.rev_complement(kmer[0])):
-                probe_name = f"PROBE_{probe_idx}_RV"
+                probe_name = f"PROBE_{probe_idx}_RIGHT"
                 three_prime_penalty = primers.calc_3_prime_penalty("-", per_base_mismatches)
                 probe_candidates[probe_name] = [primers.rev_complement(kmer[0]), kmer[1], kmer[2],
                                                 base_penalty + permutation_penalty + three_prime_penalty,
@@ -208,13 +208,13 @@ def assess_amplicons(left_subset, right_subset, qpcr_probes, probe, majority_con
             if not hardfilter_amplicon(majority_consensus, left_primer, right_primer):
                 continue
             # ... the probe is close enough to the primer on the same strand
-            if "FW" in probe:
+            if "LEFT" in probe:
                 if not qpcr_probes[probe][1] in range(
                         left_primer[2] + config.QPROBE_DISTANCE[0],
                         left_primer[2] + config.QPROBE_DISTANCE[1] + 1
                 ):
                     continue
-            elif "RV" in probe:
+            elif "RIGHT" in probe:
                 if not right_primer[1] in range(
                         qpcr_probes[probe][2] + config.QPROBE_DISTANCE[0],
                         qpcr_probes[probe][2] + config.QPROBE_DISTANCE[1] + 1

{varvamp-1.1.dist-info → varvamp-1.1.2.dist-info}/METADATA

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

@@ -0,0 +1,21 @@
+varvamp/__init__.py,sha256=K5ccRm45N-jlwv4_LFmzwr4rl9NgmWICL5kNY_00-RE,107
+varvamp/__main__.py,sha256=9R3mbX2_Q5LByPx8WLoTbvZ-G2dbRSMpDlgze0Wm5Fc,98
+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=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-1.1.2.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.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
 

varvamp-1.1.dist-info/RECORD

@@ -1,21 +0,0 @@
-varvamp/__init__.py,sha256=yXk-Pc_9lP6OKb_nKDf6v1kYmUk-XV6BGIsiiODP1WY,105
-varvamp/__main__.py,sha256=9R3mbX2_Q5LByPx8WLoTbvZ-G2dbRSMpDlgze0Wm5Fc,98
-varvamp/command.py,sha256=Zz605uDIUyipibYT95P1fG0RtVyEF6yIYmpKezP-QXA,18445
-varvamp/scripts/__init__.py,sha256=DtRsgfnA60BvccKMuD-Ueo1UpxaeANUfIWxGi1xPcV0,46
-varvamp/scripts/alignment.py,sha256=w2I7BnaUt_rh1EaDQaU9Q_dmL_q019NtnaC8YMccOgM,7317
-varvamp/scripts/blast.py,sha256=unkBLKRHv6v1BAsMyud47oTTW70SxAp2qAtFSbW3rqA,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/param_estimation.py,sha256=jpfmbjCFp23V07af3y1uO2dQZJiWLlyOBa11aMphkko,3694
-varvamp/scripts/primers.py,sha256=Ys6sgOlPblgX05BNLWxySTXrmJ2HksDfu3v-WKugcBM,13423
-varvamp/scripts/qpcr.py,sha256=5j7jIkAIykwCGVVReC0oQn7TxcXD_sKqLTf2wpo6rws,14473
-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.dist-info/METADATA,sha256=Ggrco8P309OMt_-LeU56LL5YZk8asSKDSpM-K7MjkGI,5147
-varvamp-1.1.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-varvamp-1.1.dist-info/entry_points.txt,sha256=puzW-basyBexZT4JVRUfUEqobvFmEyfqRQaqFjp7rB0,49
-varvamp-1.1.dist-info/top_level.txt,sha256=11oVwE3SBUB9aTmvpvEDru95Tc5GZqQikzzFjw2eVGc,8
-varvamp-1.1.dist-info/RECORD,,