smaller changes

example_mave_data/MaveBindRBD.csv

@@ -1,4 +1,4 @@
-accession,hgvs_nt,hgvs_splice,hgvs_pro,score,average,library,AA
+exaccession,hgvs_nt,hgvs_splice,hgvs_pro,score,average,library,AA
 urn:mavedb:00000044-a-1#7954,NA,NA,p.Lys199Val,0.09,0.07,2,K529V
 urn:mavedb:00000044-a-1#7955,NA,NA,p.Lys199Trp,-0.02,0,1,K529W
 urn:mavedb:00000044-a-1#7956,NA,NA,p.Lys199Trp,0.01,0,2,K529W

virheat/__init__.py

@@ -1,3 +1,3 @@
 """plot vcf data as a heatmap mapped to a virus genome"""
 _program = "virheat"
-__version__ = "0.7"
+__version__ = "0.7.1"

virheat/command.py

@@ -36,7 +36,8 @@ def get_args(sysargs):
         "-r",
         "--reference",
         type=str,
-        metavar="None",
+        metavar="ref_id",
+        required=True,
         default=None,
         help="reference identifier"
     )
@@ -155,7 +156,7 @@ def main(sysargs=sys.argv[1:]):
         sys.exit("\033[31m\033[1mERROR:\033[0m No VCF files provided")
     else:
         if args.scores:
-            frequency_lists, unique_mutations, file_names = data_prep.extract_vcf_data(vcf_files, threshold=args.threshold, scores=True)
+            frequency_lists, unique_mutations, file_names = data_prep.extract_vcf_data(vcf_files, args.reference, threshold=args.threshold, scores=True)
             n_scores = len(args.scores)
         else:
             frequency_lists, unique_mutations, file_names = data_prep.extract_vcf_data(vcf_files, args.reference, threshold=args.threshold)
@@ -186,7 +187,7 @@ def main(sysargs=sys.argv[1:]):
     if args.gff3_path is not None and args.genome_length is not None:
         sys.exit("\033[31m\033[1mERROR:\033[0m Do not provide the -g and -l argument simultaneously!")
     elif args.gff3_path is not None:
-        gff3_info, gff3_ref_name = data_prep.parse_gff3(args.gff3_path, args.reference)
+        gff3_info = data_prep.parse_gff3(args.gff3_path, args.reference)
         genome_end = data_prep.get_genome_end(gff3_info)
         genes_with_mutations, n_tracks = data_prep.create_track_dict(unique_mutations, gff3_info, args.gff3_annotations)
     elif args.genome_length is not None:

virheat/scripts/data_prep.py

@@ -62,10 +62,10 @@ def read_vcf(vcf_file, reference):
         header = header_lines[0]
     # get each line as frequency_lists
     with open(vcf_file, "r") as f:
-        lines = [l.split("\t") for l in f if not l.startswith('#') and l.startswith(reference)]
+        lines = [l.split("\t") for l in f if l.startswith(reference)]
     # check if vcf is empty
     if not lines:
-        print(f"\033[31m\033[1mWARNING:\033[0m {vcf_file} has no variants with {reference} as #CHROM!")
+        print(f"\033[31m\033[1mWARNING:\033[0m {vcf_file} has no variants to {reference}!")
     # get standard headers as keys
     for key in header[0:6]:
         vcf_dict[key] = []
@@ -139,7 +139,7 @@ def extract_vcf_data(vcf_files, reference, threshold=0, scores=False):
         {x[0] for li in frequency_lists for x in li}, key=lambda x: int(x.split("_")[0])
     )
     if not unique_mutations:
-        sys.exit(f"\033[31m\033[1mERROR:\033[0m No unique mutations to {reference} found in all vcf files!")
+        sys.exit(f"\033[31m\033[1mERROR:\033[0m No variants to {reference} in all vcf files!")
 
     return frequency_lists, unique_mutations, file_names
 
@@ -279,12 +279,9 @@ def parse_gff3(file, reference):
     with open(file, "r") as gff3_file:
         for line in gff3_file:
             # ignore comments and last line
-            if line.startswith("#") or line == "\n":
+            if not line.startswith(reference):
                 continue
             gff_values = line.split("\t")
-            if gff_values[0] != reference:
-                continue
-            gff3_ref_name = gff_values[0]
             # create keys
             if gff_values[2] not in gff3_dict:
                 gff3_dict[gff_values[2]] = {}
@@ -307,7 +304,7 @@ def parse_gff3(file, reference):
     if not gff3_dict:
         sys.exit(f"\033[31m\033[1mERROR:\033[0m {reference} not found in gff3 file.")
 
-    return gff3_dict, gff3_ref_name
+    return gff3_dict
 
 
 def get_genome_end(gff3_dict):