Merge branch 'main' of github.com:faircloth-lab/phyluce

.github/workflows/main.yml

@@ -29,7 +29,7 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Set up Python
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v4
         with:
           python-version: 3.6
 

bin/assembly/phyluce_assembly_explode_get_fastas_file

@@ -46,7 +46,10 @@ def get_args():
         help="""Split file by taxon and not by locus""",
     )
     parser.add_argument(
-        "--split-char", type=str, default="_", help="""The character to split on"""
+        "--split-char",
+        type=str,
+        default="_",
+        help="""The character to split on""",
     )
     return parser.parse_args()
 
@@ -66,13 +69,13 @@ def main():
         os.makedirs(args.output)
     print("Reading fasta...")
     if not args.by_taxon:
-        with open(args.input, "rU") as input:
-            for seq in SeqIO.parse(input, "fasta"):
+        with open(args.input, "rU") as input_file:
+            for seq in SeqIO.parse(input_file, "fasta"):
                 uce = seq.id.split(args.split_char)[0]
                 seqdict[uce].append(seq)
     elif args.by_taxon:
-        with open(args.input, "rU") as input:
-            for seq in SeqIO.parse(input, "fasta"):
+        with open(args.input, "rU") as input_file:
+            for seq in SeqIO.parse(input_file, "fasta"):
                 taxon = "-".join(seq.id.split(args.split_char)[1:])
                 seqdict[taxon].append(seq)
     print("Writing fasta...")

phyluce/tests/test_match_contigs.py

@@ -162,6 +162,6 @@ def test_match_contigs_to_barcodes(o_dir, e_dir, request):
         re.search("(Best.*\n)", stdout.decode("utf-8")).groups()[0].strip()
     )
     assert (
-        "Best BOLD systems match for locus comp17283_c0_seq1: Anas poecilorhyncha [GBIR3505-13]"
+        "Best BOLD systems match for locus comp17283_c0_seq1: Anas platyrhynchos [TZBNA296-03]"
         in observed
     )