Changed bed file structure to ARTICv3 (#42)

* changed requirements txt to inhibit incomp

* added --name option and now bed primer files are reported in ARTIC v3 style

* updated docs

* changed pool indexing to +1

* comma fix

* small changes in main

* changed type var shadowing

* removed not needed variable

* further code cleanup

* small fixes in goodbye message

* fixed BLAST reporting error due to not defined variable

README.md

@@ -43,7 +43,7 @@ For a lot of virus genera it is difficult to design pan-specific primers. varVAM
 
 We, in collaboration with specialists for the respective viruses, have already designed and wet-lab evaluated primer schemes for various viral pathogens. All the input data and varVAMP outputs are freely available [here](https://github.com/jonas-fuchs/ViralPrimerSchemes). 
 
-If you design primers for a particular pathogen, we will be happy to include them in this repo and make it freely available. Just contribute via an issue or pull request!
+Moreover, varVAMP primers are now available at [primerschemes](https://labs.primalscheme.com/). varVAMP now reports primer bed files in ARTICv3 format. Feel free to contribute newly designed schemes via this [Github repository of the QuickLab](https://github.com/quick-lab/primerschemes). Use [primal-page](https://github.com/ChrisgKent/primal-page) developed by [Chris Kent](https://github.com/ChrisgKent) to generate data for compatible pull-requests.
 
 # Citing varVAMP
 

docs/installation.md

@@ -21,7 +21,8 @@ pip install setuptools varvamp
 ### CONDA:
 
 ```shell
-conda install -c bioconda varvamp
+conda create -n varvamp varvamp
+conda activate varvamp
 ```
 
 ### DOCKER:

docs/usage.md

@@ -43,6 +43,7 @@ optional arguments:
   -a , --n-ambig        	max number of ambiguous characters in a primer
   -db None, --database None     location of the BLAST db
   -th 1, --threads 1            number of threads
+  --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
   -n inf, --report-n inf	report the top n best hits
@@ -58,6 +59,7 @@ optional arguments:
   -a , --n-ambig        	max number of ambiguous characters in a primer
   -db None, --database None     location of the BLAST db
   -th 1, --threads 1	        number of threads
+  --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
@@ -73,6 +75,7 @@ optional arguments:
   -a , --n-ambig        	max number of ambiguous characters in a primer
   -db None, --database None     location of the BLAST db
   -th 1, --threads 1   	        number of threads
+  --name varVAMP                name of the scheme
   -pa , --pn-ambig   		max number of ambiguous characters in a probe
   -n 50, --test-n 50    	test the top n qPCR amplicons for secondary structures at the minimal primer temperature
   -d -3, --deltaG -3            minimum free energy (kcal/mol/K) cutoff at the lowest primer melting temp

requirements.txt

@@ -1,6 +1,6 @@
-biopython>=1.79
-matplotlib>=3.5.1
-primer3-py>=1.1.0
-pandas>=1.4.4
-numpy>=1.23.3
-seqfold>=0.7.15
+biopython~=1.79
+matplotlib~=3.5.1
+primer3-py~=1.1.0
+pandas~=1.4.4
+numpy~=1.23.3
+seqfold~=0.7.15

varvamp/__init__.py

@@ -1,3 +1,3 @@
 """Tool to design amplicons for highly variable virusgenomes"""
 _program = "varvamp"
-__version__ = "1.2.0"
+__version__ = "1.2.1"

varvamp/command.py

@@ -89,6 +89,13 @@ def get_args(sysargs):
             type=int,
             default=1
         )
+        par.add_argument(
+            "--name",
+            help="name of the scheme",
+            metavar="varVAMP",
+            type=str,
+            default="varVAMP"
+        )
     for par in (SINGLE_parser, TILED_parser):
         par.add_argument(
             "-ol",
@@ -261,10 +268,10 @@ def shared_workflow(args, log_file):
         ambiguous_consensus,
         alignment_cleaned
     )
-    for type, primer_candidates in [("+", left_primer_candidates), ("-", right_primer_candidates)]:
+    for primer_type, primer_candidates in [("+", left_primer_candidates), ("-", right_primer_candidates)]:
         if not primer_candidates:
             logging.raise_error(
-                f"no {type} primers found.\n",
+                f"no {primer_type} primers found.\n",
                 log_file,
                 exit=True
             )
@@ -330,7 +337,7 @@ def single_and_tiled_shared_workflow(args, left_primer_candidates, right_primer_
     return all_primers, amplicons
 
 
-def single_workflow(args, amplicons, all_primers, log_file):
+def single_workflow(args, amplicons, log_file):
     """
     workflow part specific for single mode
     """
@@ -477,13 +484,13 @@ def qpcr_workflow(args, data_dir, alignment_cleaned, ambiguous_consensus, majori
     return probe_regions, final_schemes
 
 
-def main(sysargs=sys.argv[1:]):
+def main():
     """
     main varvamp workflow
     """
 
     # start varVAMP
-    args = get_args(sysargs)
+    args = get_args(sys.argv[1:])
     if not args.verbose:
         sys.stdout = open(os.devnull, 'w')
     start_time = datetime.datetime.now()
@@ -496,10 +503,10 @@ def main(sysargs=sys.argv[1:]):
     alignment_cleaned, majority_consensus, ambiguous_consensus, primer_regions, left_primer_candidates, right_primer_candidates = shared_workflow(args, log_file)
 
     # write files that are shared in all modes
-    reporting.write_regions_to_bed(primer_regions, data_dir)
+    reporting.write_regions_to_bed(primer_regions, args.name, data_dir)
     reporting.write_alignment(data_dir, alignment_cleaned)
-    reporting.write_fasta(data_dir, "majority_consensus", majority_consensus)
-    reporting.write_fasta(results_dir, "ambiguous_consensus", ambiguous_consensus)
+    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)
 
     # 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,
@@ -526,7 +533,6 @@ def main(sysargs=sys.argv[1:]):
             amplicon_scheme = single_workflow(
                 args,
                 amplicons,
-                all_primers,
                 log_file
             )
         elif args.mode == "tiled":
@@ -549,22 +555,24 @@ def main(sysargs=sys.argv[1:]):
         else:
             # make sure amplicons with no off-target products and with low penalties get the lowest numbers
             amplicon_scheme.sort(key=lambda x: (x.get("off_targets", False), x["penalty"]))
-        reporting.write_all_primers(data_dir, all_primers)
+        reporting.write_all_primers(data_dir, args.name, all_primers)
         reporting.write_scheme_to_files(
             results_dir,
             amplicon_scheme,
             ambiguous_consensus,
+            args.name,
             args.mode,
             log_file
         )
         reporting.varvamp_plot(
             results_dir,
             alignment_cleaned,
             primer_regions,
+            args.name,
             all_primers=all_primers,
             amplicon_scheme=amplicon_scheme,
         )
-        reporting.per_base_mismatch_plot(results_dir, amplicon_scheme, args.threshold)
+        reporting.per_base_mismatch_plot(results_dir, amplicon_scheme, args.threshold, args.name)
 
     # QPCR mode
     if args.mode == "qpcr":
@@ -583,16 +591,17 @@ def main(sysargs=sys.argv[1:]):
 
         # make sure amplicons with no off-target products and with low penalties get the lowest numbers
         final_schemes.sort(key=lambda x: (x.get("off_targets", False), x["penalty"]))
-        reporting.write_regions_to_bed(probe_regions, data_dir, "probe")
-        reporting.write_qpcr_to_files(results_dir, final_schemes, ambiguous_consensus, log_file)
+        reporting.write_regions_to_bed(probe_regions, args.name, data_dir, "probe")
+        reporting.write_qpcr_to_files(results_dir, final_schemes, ambiguous_consensus, args.name, log_file)
         reporting.varvamp_plot(
             results_dir,
             alignment_cleaned,
             primer_regions,
+            args.name,
             probe_regions=probe_regions,
             amplicon_scheme=final_schemes
         )
-        reporting.per_base_mismatch_plot(results_dir, final_schemes, args.threshold, mode="QPCR")
+        reporting.per_base_mismatch_plot(results_dir, final_schemes, args.threshold, args.name, mode="QPCR")
 
     # varVAMP finished
     logging.varvamp_progress(log_file, progress=1, start_time=start_time)

varvamp/scripts/logging.py

@@ -15,12 +15,12 @@
 from varvamp import __version__
 
 
-def create_dir_structure(dir):
+def create_dir_structure(dir_path):
     """
     create output folders and log file
     """
     cwd = os.getcwd()
-    results_dir = os.path.join(cwd, dir)
+    results_dir = os.path.join(cwd, dir_path)
     data_dir = os.path.join(results_dir, "data/")
     # create folders
     if not os.path.exists(results_dir):
@@ -567,7 +567,7 @@ def goodbye_message():
         "Thank you. Come again.",
         ">Placeholder for your advertisement<",
         "Make primers great again!",
-        "Ciao cacao!"
+        "Ciao cacao!",
         "And now lets pray to the PCR gods.",
         "**bibobibobop** task finished",
         "Thank you for traveling with varVAMP.",
@@ -581,5 +581,14 @@ def goodbye_message():
         "Barba non facit philosophum.",
         "Task failed successfully.",
         "Never gonna give you up, never gonna let you down.",
+        "Have you tried turning it off and on again?",
+        "Look, I am your primer scheme.",
+        "Quod erat demonstrandum.",
+        "Miau?",
+        "This is an automated message informing you that you are awsome.",
+        "Why was the negative-sense virus angry at the positive-sense virus?\nBecause he was left stranded!",
+        "If you see this message twice, you are an experienced user.",
+        "No one expects the spanish inquisition!",
+        "Primer design you must."
     ]
     print(f"\n{random.choice(messages)}")