diff --git a/rescript/tests/test_trim_alignment.py b/rescript/tests/test_trim_alignment.py index 2c17b55..eb6603b 100644 --- a/rescript/tests/test_trim_alignment.py +++ b/rescript/tests/test_trim_alignment.py @@ -14,14 +14,13 @@ AlignedDNAFASTAFormat, DNAIterator,) -from qiime2.plugins import alignment +from qiime2.plugins.alignment.methods import mafft_add from rescript.trim_alignment import ( _prepare_positions, _process_primers, _locate_primer_positions, _trim_all_sequences, _trim_alignment) import_data = qiime2.Artifact.import_data -expand_aln = alignment.actions.mafft_add class FakeCtx: @@ -275,7 +274,7 @@ def test_trim_all_sequences_no_rev(self): # tests against expected alignment length def test_trim_alignment_keeplen_false(self): obs_v4_nokeep_aln = _trim_alignment( - expand_aln, + mafft_add, self.aligned_silva_seqs_art, self.v4_primers_dict["forward"], self.v4_primers_dict["reverse"], @@ -292,7 +291,7 @@ def test_trim_alignment_keeplen_false(self): # tests against expected alignment length def test_trim_alignment_keeplen_true(self): obs_v4_keep_aln = _trim_alignment( - expand_aln, + mafft_add, self.aligned_silva_seqs_art, self.v4_primers_dict["forward"], self.v4_primers_dict["reverse"],