Change to fasta header logic

Author: BioWilko

artic/fasta_header.py

@@ -1,16 +1,18 @@
 from Bio import SeqIO
+from importlib.metadata import version
 
 
 def fasta_header(args):
     with open(args.filename) as fh:
         rec = list(SeqIO.parse(fh, "fasta"))
 
     fasta_format = "fasta-2line" if args.linearise_fasta else "fasta"
+    artic_version = version("artic")
 
     with open(args.filename, "w") as fh:
         for record in rec:
             chrom = record.id
-            record.id = f"{args.samplename}/{chrom}/ARTIC/{args.caller}"
+            record.id = f"{args.samplename} {chrom}_artic-network/fieldbioinformatics_{artic_version}"
 
             SeqIO.write(record, fh, fasta_format)
 

artic/minion.py

@@ -121,7 +121,7 @@ def run(parser, args):
         raise SystemExit(1)
 
     ## collect the primer pools
-    pools = set([row["PoolName"] for row in read_bed_file(bed)])
+    pools = set([row["PoolName"] for row in read_bed_file(bed)] + ["unmatched"])
 
     ## create a holder to keep the pipeline commands in
     cmds = []