tests pip

EBI-Metagenomics · Oct 7, 2024 · 47fcfa9 · 47fcfa9
1 parent be6e440
commit 47fcfa9
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/bin/write_viral_gff.py b/bin/write_viral_gff.py
@@ -6,7 +6,7 @@
 import gzip
 import csv
 
-from parse_viral_pred import Record
+from bin.parse_viral_pred import Record
 
 from Bio import SeqIO
 

diff --git a/tests/test_parse_viral_preds.py b/tests/test_parse_viral_preds.py
@@ -102,7 +102,7 @@ def test_parsing_with_dups(self):
 
         vs_files = [os.path.join(vs_path, f) for f in os.listdir(vs_path)]
 
-        hc, lc, pp, *_ = merge_annotations(pprmeta_path, vf_path, vs_files, assembly)
+        hc, lc, pp, *_ = merge_annotations(pprmeta_path, vf_path, vs_files, None, assembly)
 
         hc_ids = set([h.id for h in hc])
         lc_ids = set([l.id for l in lc])
@@ -129,7 +129,7 @@ def test_full(self):
 
         print(test_dir)
 
-        main(pprmeta_path, vf_path, vs_files, assembly, test_dir)
+        main(pprmeta_path, vf_path, vs_files, None, assembly, test_dir, 0.9)
 
         with open(test_dir + "/high_confidence_viral_contigs.fna", "rb") as hc_f:
             with open(
@@ -176,7 +176,7 @@ def test_virsorter_precedence(self):
 
         sorter_files = [os.path.join(vs_path, f) for f in os.listdir(vs_path)]
 
-        main(pprmeta_path, vf_path, sorter_files, assembly, test_dir)
+        main(pprmeta_path, vf_path, sorter_files, None, assembly, test_dir, 0.9)
 
         with open(test_dir + "/high_confidence_viral_contigs.fna", "rb") as hc_f:
             with open(