make synthetic_v1_chr-10.fam/bim into local sample files

fastlmm · Jan 18, 2024 · db27874 · db27874
1 parent 70cc25e
commit db27874
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Showing 3 changed files with 16 additions and 11 deletions.
diff --git a/bed_reader/_sample_data.py b/bed_reader/_sample_data.py
@@ -14,9 +14,9 @@
         path=pooch.os_cache("bed_reader"),
         # The remote data is on Github
         base_url="https://raw.githubusercontent.com/"
-        + "fastlmm/bed-reader/Oct2023/bed_reader/tests/data/",
+        + "fastlmm/bed-sample-files/main/",
         # If this is a development version, get the data from the master branch
-        version_dev="master",
+        version_dev="main",
         # The registry specifies the files that can be fetched
         env="BED_READER_DATA_DIR",
     )

diff --git a/bed_reader/tests/registry.txt b/bed_reader/tests/registry.txt
@@ -37,3 +37,5 @@ toydata.5chrom.fam 9551c70290580c9b23cb83c98ccc7791f380169bdaddfbc2edb905ff78879
 sparse.bed 70f76a3920b4c8498ecfae9c8837c3ea841a874f88f60c082141905a24d63114
 sparse.fam 729bb46dab41082c6b5937f7f9e3a68d0c0f27d2ad795f1fa1fd146354fb6aa7
 sparse.bim 77917e8645ce0744a7d89bfca0d78a594a8e3d5640a4bf90ceae3c1ab2ea5479
+synthetic_v1_chr-10.fam 394bd3da24760327d6103466cb83002dde25440a650e667cf1597d471fd73fea
+synthetic_v1_chr-10.bim 0f889d32bb183de0d26581ae59d94058204645f3325d78fe4cb96156d9792ac9
diff --git a/bed_reader/tests/test_open_bed_cloud.py b/bed_reader/tests/test_open_bed_cloud.py
@@ -14,8 +14,6 @@
 
 
 def test_cloud_read1(shared_datadir):
-    import math
-
     file = shared_datadir / "plink_sim_10s_100v_10pmiss.bed"
     file = PurePath(file).as_uri()
 
@@ -1068,17 +1066,22 @@ def test_http_one():
 
 
 def test_http_two():
+    from bed_reader import open_bed, sample_file
+
+    local_fam_file = sample_file("synthetic_v1_chr-10.fam")
+    local_bim_file = sample_file("synthetic_v1_chr-10.bim")
     with open_bed(
-        "https://www.ebi.ac.uk/biostudies/files/S-BSST936/example/synthetic_small_v1_chr-10.bed",
-        fam_filepath=r"C:\Users\carlk\Downloads\S-BSST936\example\synthetic_small_v1_chr-10.fam",
-        bim_filepath=r"C:\Users\carlk\Downloads\S-BSST936\example\synthetic_small_v1_chr-10.bim",
+        "https://www.ebi.ac.uk/biostudies/files/S-BSST936/genotypes/synthetic_v1_chr-10.bed",
+        fam_filepath=local_fam_file,
+        bim_filepath=local_bim_file,
         skip_format_check=True,
     ) as bed:
-        print(bed.iid[:5])
-        print(bed.sid[:5])
-        print(np.unique(bed.chromosome))
+        print(f"iid_count={bed.iid_count:_}, sid_count={bed.sid_count:_}")
+        print(f"iid={bed.iid[:5]}...")
+        print(f"sid={bed.sid[:5]}...")
+        print(f"unique chromosomes = {np.unique(bed.chromosome)}")
         val = bed.read(index=np.s_[:10, :: bed.sid_count // 10])
-        print(val)
+        print(f"val={val}")
         assert val.shape == (10, 10) or val.shape == (10, 11)