varvamp 1.1__tar.gz → 1.1.2__tar.gz

{varvamp-1.1 → varvamp-1.1.2}/PKG-INFO

@@ -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 → varvamp-1.1.2}/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-1.1 → varvamp-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-1.1 → varvamp-1.1.2}/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-1.1 → varvamp-1.1.2}/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 → varvamp-1.1.2}/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-1.1 → varvamp-1.1.2}/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 → varvamp-1.1.2}/varvamp.egg-info/PKG-INFO

@@ -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