enforced overlap between amplicon inserts in tiled mode (#43)

* enforced overlap between amplicon inserts in tiled mode

* renamed consensus files to differentiate between majority and ambi consensus. also changed respective bed files

* reverted bed header for tiled schemes as this might cause problems with several other programs

docs/usage.md

@@ -62,7 +62,7 @@ optional arguments:
   --name varVAMP                name of the scheme
   -ol 1000, --opt-length 1000	optimal length of the amplicons
   -ml 1500, --max-length 1500	max length of the amplicons
-  -o 100, --overlap 100		min overlap of the amplicons
+  -o 100, --overlap 100		min overlap of the amplicon inserts
 ```
 **qpcr** mode:
 ```shell

varvamp/__init__.py

@@ -1,3 +1,3 @@
 """Tool to design amplicons for highly variable virusgenomes"""
 _program = "varvamp"
-__version__ = "1.2.1"
+__version__ = "1.2.2"

varvamp/command.py

@@ -119,7 +119,7 @@ def get_args(sysargs):
         type=int,
         metavar="100",
         default=100,
-        help="min overlap of the amplicons"
+        help="min overlap of the amplicon inserts"
     )
     SINGLE_parser.add_argument(
         "-n",
@@ -505,8 +505,8 @@ def main():
     # write files that are shared in all modes
     reporting.write_regions_to_bed(primer_regions, args.name, data_dir)
     reporting.write_alignment(data_dir, alignment_cleaned)
-    reporting.write_fasta(data_dir, f"majority_consensus", f"{args.name}_consensus",majority_consensus)
-    reporting.write_fasta(results_dir, f"ambiguous_consensus", f"{args.name}_consensus", ambiguous_consensus)
+    reporting.write_fasta(data_dir, f"majority_consensus", f"{args.name}_majority_consensus",majority_consensus)
+    reporting.write_fasta(results_dir, f"ambiguous_consensus", f"{args.name}_ambiguous_consensus", ambiguous_consensus)
 
     # Functions called from here on return lists of amplicons that are refined step-wise into final schemes.
     # These lists that are passed between functions and later used for reporting consist of dictionary elemnts,

varvamp/scripts/logging.py

@@ -147,7 +147,7 @@ def raise_arg_errors(args, log_file):
                 log_file,
                 exit=True
             )
-        if args.overlap < 50:
+        if args.overlap < 10:
             raise_error(
                 "small overlaps might hinder downstream analyses. Consider increasing.",
                 log_file

varvamp/scripts/reporting.py

@@ -53,7 +53,7 @@ def write_regions_to_bed(primer_regions, scheme_name, path, mode=None):
     with open(outfile, 'w') as o:
         for counter, region in enumerate(primer_regions):
             print(
-                f"{scheme_name}_consensus",
+                f"{scheme_name}_ambiguous_consensus",
                 region[0],
                 region[1],
                 "REGION_"+str(counter),
@@ -68,9 +68,7 @@ def write_primers_to_bed(outfile, scheme_name, primer_name, primer_properties, n
     """
     with open(outfile, 'a') as o:
         # write header for primer bed
-        if os.path.getsize(outfile) == 0 and sequence is not None:
-            print("#chrom\tchromStart\tchromEnd\tprimer-name\tpool\tstrand\tprimer-sequence", file=o)
-        data = [f"{scheme_name}_consensus",
+        data = [f"{scheme_name}_ambiguous_consensus",
             primer_properties[1],  # start
             primer_properties[2],  # stop
             primer_name,
@@ -150,7 +148,7 @@ def write_qpcr_to_files(path, final_schemes, ambiguous_consensus, scheme_name, l
             amp_name = f"{scheme_name}_{n}"
             # write bed amplicon file
             print(
-                f"{scheme_name}_consensus",
+                f"{scheme_name}_ambiguous_consensus",
                 amp["LEFT"][1],
                 amp["RIGHT"][2],
                 amp_name,
@@ -329,7 +327,7 @@ def write_scheme_to_files(path, amplicon_scheme, ambiguous_consensus, scheme_nam
         # write amplicon bed with amplicons sorted by start position
         for record in sorted(amplicon_bed_records, key=lambda x: x[0]):
             print(
-                f"{scheme_name}_consensus",
+                f"{scheme_name}_ambiguous_consensus",
                 *record,
                 ".",
                 sep="\t",

varvamp/scripts/scheme.py

@@ -102,14 +102,14 @@ def create_amplicon_graph(amplicons, min_overlap):
 
     # add the maximum len of a primer to ensure that possible amplicon starts
     # before the min overlap
-    min_overlap = min_overlap + config.PRIMER_SIZES[2]
+    min_overlap = min_overlap + config.PRIMER_SIZES[1]
 
     for current_amplicon in amplicons:
         # remember all vertices
         amplicon_id = current_amplicon["id"]
         nodes.append(amplicon_id)
         start = current_amplicon["LEFT"][1] + current_amplicon["length"]/2
-        stop = current_amplicon["RIGHT"][2] - min_overlap
+        stop = current_amplicon["RIGHT"][1] - min_overlap
         for next_amplicon in amplicons:
             # check if the next amplicon lies within the start/stop range of
             # the current amplicon and if its non-overlapping part is large