Skip to content

Commit

Permalink
test: update reference path (bis)
Browse files Browse the repository at this point in the history
  • Loading branch information
cmdoret committed Oct 21, 2024
1 parent f1440f3 commit 8d135c5
Showing 1 changed file with 4 additions and 2 deletions.
6 changes: 4 additions & 2 deletions tests/test_api_local.py
Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,8 @@

from modos.api import MODO

REF_PATH = "data/ex/reference.fa"

## Initialize modo


Expand Down Expand Up @@ -112,7 +114,7 @@ def test_stream_genomics_no_region(test_modo):
modo_files = [str(fi) for fi in test_modo.list_files()]
file_path = list(filter(lambda x: re.search(r"cram$", x), modo_files))
seq = test_modo.stream_genomics(
file_path=file_path[0], reference_filename="data/ex/reference1.fa"
file_path=file_path[0], reference_filename=REF_PATH
)
assert isinstance(seq, Iterator)
assert isinstance(next(seq), pysam.AlignedSegment)
Expand All @@ -124,7 +126,7 @@ def test_stream_genomics_region(test_modo):
seq = test_modo.stream_genomics(
file_path=file_path[0],
region="BA000007.3",
reference_filename="data/ex/reference.fa",
reference_filename=REF_PATH,
)
assert isinstance(seq, Iterator)
assert isinstance(next(seq), pysam.AlignedSegment)

0 comments on commit 8d135c5

Please sign in to comment.