diff --git a/tests/data/snp/.gitignore b/tests/data/snp/.gitignore new file mode 100644 index 0000000..355164c --- /dev/null +++ b/tests/data/snp/.gitignore @@ -0,0 +1 @@ +*/ diff --git a/tests/data/snp/kidney_eqtl.vcf b/tests/data/snp/kidney_eqtl.vcf new file mode 100644 index 0000000..c3760fb --- /dev/null +++ b/tests/data/snp/kidney_eqtl.vcf @@ -0,0 +1,55 @@ +##fileformat=VCFv4.2 +chr1 16693559 chr1_16693559_C_T_b38 C T . . +chr1 25235176 chr1_25235176_G_A_b38 G A . . +chr1 121041638 chr1_121041638_C_T_b38 C T . . +chr2 48595242 chr2_48595242_G_A_b38 G A . . +chr2 62506118 chr2_62506118_C_T_b38 C T . . +chr2 74958729 chr2_74958729_G_T_b38 G T . . +chr2 108288574 chr2_108288574_C_T_b38 C T . . +chr2 110607190 chr2_110607190_G_A_b38 G A . . +chr2 127648067 chr2_127648067_C_T_b38 C T . . +chr2 131682500 chr2_131682500_G_C_b38 C G . . +chr2 161244750 chr2_161244750_G_A_b38 G A . . +chr3 69105192 chr3_69105192_C_G_b38 G C . . +chr5 5078200 chr5_5078200_C_T_b38 C T . . +chr5 71044045 chr5_71044045_G_T_b38 G T . . +chr5 181003797 chr5_181003797_T_C_b38 T C . . +chr6 85678170 chr6_85678170_G_T_b38 T G . . +chr6 106629627 chr6_106629627_G_A_b38 G A . . +chr6 111592059 chr6_111592059_C_T_b38 C T . . +chr6 130053316 chr6_130053316_T_A_b38 A T . . +chr6 135302695 chr6_135302695_C_T_b38 C T . . +chr7 30612322 chr7_30612322_G_A_b38 A G . . +chr7 95596945 chr7_95596945_T_C_b38 T C . . +chr9 62885682 chr9_62885682_A_G_b38 A G . . +chr10 45832504 chr10_45832504_G_C_b38 G C . . +chr10 48022458 chr10_48022458_G_A_b38 G A . . +chr10 45947840 chr10_45947840_C_T_b38 C T . . +chr11 1941470 chr11_1941470_C_T_b38 C T . . +chr14 73787509 chr14_73787509_G_A_b38 G A . . +chr14 94129652 chr14_94129652_T_C_b38 T C . . +chr15 95130166 chr15_95130166_G_A_b38 A G . . +chr15 99733402 chr15_99733402_G_C_b38 C G . . +chr15 100574435 chr15_100574435_T_C_b38 T C . . +chr16 1215891 chr16_1215891_G_A_b38 G A . . +chr16 2936322 chr16_2936322_T_C_b38 C T . . +chr16 11976565 chr16_11976565_T_C_b38 C T . . +chr16 14912068 chr16_14912068_C_T_b38 C T . . +chr16 18339330 chr16_18339330_G_C_b38 G C . . +chr16 70251998 chr16_70251998_A_G_b38 A G . . +chr16 84180359 chr16_84180359_G_A_b38 G A . . +chr17 4443684 chr17_4443684_T_C_b38 C T . . +chr17 6700205 chr17_6700205_T_C_b38 T C . . +chr17 15976596 chr17_15976596_C_T_b38 T C . . +chr17 40720995 chr17_40720995_T_C_b38 T C . . +chr17 50547162 chr17_50547162_A_C_b38 A C . . +chr19 44662645 chr19_44662645_A_C_b38 C A . . +chr19 44718265 chr19_44718265_T_C_b38 C T . . +chr19 57438168 chr19_57438168_T_C_b38 C T . . +chr22 17199629 chr22_17199629_A_C_b38 A C . . +chr22 18531430 chr22_18531430_G_A_b38 A G . . +chr22 21468436 chr22_21468436_T_C_b38 C T . . +chr22 21980728 chr22_21980728_T_C_b38 T C . . +chr22 24002141 chr22_24002141_T_G_b38 G T . . +chr22 50562842 chr22_50562842_G_A_b38 G A . . +chrX 153060001 chrX_153060001_G_A_b38 G A . . diff --git a/tests/test_snp.py b/tests/test_snp.py index e44cf44..a922fbd 100644 --- a/tests/test_snp.py +++ b/tests/test_snp.py @@ -10,13 +10,13 @@ params_file = "tests/data/eval/params.json" model_file = "tests/data/eval/model.h5" targets_file = "tests/data/tiny/hg38/targets.txt" -out_dir = "tests/data/snp" -vcf_file = "/home/drk/seqnn/data/gtex_fine/susie_pip90/Kidney_Cortex_pos.vcf" +snp_dir = "tests/data/snp" +vcf_file = f"{snp_dir}/kidney_eqtl.vcf" fasta_file = "%s/assembly/ucsc/hg38.fa" % os.environ["HG38"] stat_keys = ["logSAD", "logD2"] def test_snp(): - test_out_dir = f"{out_dir}/full" + test_out_dir = f"{snp_dir}/full" scores_file = f"{test_out_dir}/scores.h5" if os.path.isfile(scores_file): os.remove(scores_file) @@ -47,8 +47,8 @@ def test_snp(): def test_slice(): - test_full_dir = f"{out_dir}/full" - test_slice_dir = f"{out_dir}/sub" + test_full_dir = f"{snp_dir}/full" + test_slice_dir = f"{snp_dir}/sub" os.makedirs(test_slice_dir, exist_ok=True) scores_file = f"{test_slice_dir}/scores.h5" if os.path.isfile(scores_file):