diff options
| -rw-r--r-- | pyhegp/pyhegp.py | 38 | ||||
| -rw-r--r-- | test-data/encrypt-test-genotype-without-reference.tsv | 5 | ||||
| -rw-r--r-- | test-data/encrypt-test-summary-without-reference | 6 | ||||
| -rw-r--r-- | test-data/genotype-without-reference.tsv | 101 | ||||
| -rw-r--r-- | test-data/genotype0-without-reference.tsv | 101 | ||||
| -rw-r--r-- | test-data/genotype1-without-reference.tsv | 101 | ||||
| -rw-r--r-- | test-data/genotype2-without-reference.tsv | 101 | ||||
| -rw-r--r-- | test-data/genotype3-without-reference.tsv | 101 | ||||
| -rw-r--r-- | test-data/pool-test-summary1-without-reference | 5 | ||||
| -rw-r--r-- | test-data/pool-test-summary2-without-reference | 7 | ||||
| -rw-r--r-- | tests/test_pyhegp.py | 68 |
11 files changed, 599 insertions, 35 deletions
diff --git a/pyhegp/pyhegp.py b/pyhegp/pyhegp.py index 4e0bd84..3133c25 100644 --- a/pyhegp/pyhegp.py +++ b/pyhegp/pyhegp.py @@ -49,14 +49,22 @@ def hegp_encrypt(plaintext, key): def hegp_decrypt(ciphertext, key): return np.transpose(key) @ ciphertext +def drop_metadata_columns(genotype): + return (genotype.drop(columns=["chromosome", "position"]) + # The reference column is optional. Do not error out if it + # does not exist. + .drop(columns=["reference"], errors="ignore")) + def genotype_summary(genotype): - matrix = genotype.drop(columns=["chromosome", "position", "reference"]).to_numpy() + matrix = drop_metadata_columns(genotype).to_numpy() return Summary(genotype.shape[0], pd.DataFrame({"chromosome": genotype.chromosome, - "position": genotype.position, - "reference": genotype.reference, - "mean": np.mean(matrix, axis=1), - "std": np.std(matrix, axis=1)})) + "position": genotype.position} + | ({"reference": genotype.reference} + if "reference" in genotype.columns + else {}) + | {"mean": np.mean(matrix, axis=1), + "std": np.std(matrix, axis=1)})) def pool_stats(list_of_stats): sums = [stats.n*stats.mean for stats in list_of_stats] @@ -70,13 +78,17 @@ def pool_stats(list_of_stats): def pool_summaries(summaries): def pool_summaries2(summary1, summary2): + metadata_columns = (["chromosome", "position"] + + (["reference"] + if "reference" in summary1.data.columns + else [])) # Drop any SNPs that are not in both summaries. data = pd.merge(summary1.data.rename(columns={"mean": "mean1", "std": "std1"}), summary2.data.rename(columns={"mean": "mean2", "std": "std2"}), how="inner", - on=("chromosome", "position", "reference")) + on=metadata_columns) pooled_stats = pool_stats([Stats(summary1.n, data.mean1.to_numpy(), data.std2.to_numpy()), @@ -84,13 +96,16 @@ def pool_summaries(summaries): data.mean2.to_numpy(), data.std2.to_numpy())]) return Summary(pooled_stats.n, - pd.concat((data[["chromosome", "position", "reference"]], + pd.concat((data[metadata_columns], pd.DataFrame({"mean": pooled_stats.mean, "std": pooled_stats.std})), axis="columns")) pooled_summary = reduce(pool_summaries2, summaries) return Summary(pooled_summary.n, - pooled_summary.data.drop(columns=["reference"])) + # The reference column is optional. Do not raise an + # error if it is absent. + pooled_summary.data.drop(columns=["reference"], + errors="ignore")) def encrypt_genotype(genotype, key, summary): # Drop SNPs that have a zero standard deviation. Such SNPs have no @@ -102,8 +117,7 @@ def encrypt_genotype(genotype, key, summary): common_genotype = pd.merge(genotype, summary.data[["chromosome", "position"]], on=("chromosome", "position")) - sample_names = (common_genotype.drop( - columns=["chromosome", "position", "reference"]).columns) + sample_names = drop_metadata_columns(common_genotype).columns genotype_matrix = common_genotype[sample_names].to_numpy().T encrypted_genotype_matrix = hegp_encrypt(standardize( genotype_matrix, @@ -202,9 +216,7 @@ def encrypt_command(genotype_file, phenotype_file, summary_file, key_file, force else: summary = genotype_summary(genotype) key = random_key(np.random.default_rng(), - len(genotype - .drop(columns=["chromosome", "position", "reference"]) - .columns)) + len(drop_metadata_columns(genotype).columns)) if key_file: write_key(key_file, key) diff --git a/test-data/encrypt-test-genotype-without-reference.tsv b/test-data/encrypt-test-genotype-without-reference.tsv new file mode 100644 index 0000000..8598e36 --- /dev/null +++ b/test-data/encrypt-test-genotype-without-reference.tsv @@ -0,0 +1,5 @@ +chromosome position sample1 sample2 +chr1 1 0 1 +chr2 19 2 3 +chrX 21 4 5 +chrX 22 4 5 diff --git a/test-data/encrypt-test-summary-without-reference b/test-data/encrypt-test-summary-without-reference new file mode 100644 index 0000000..71a77a3 --- /dev/null +++ b/test-data/encrypt-test-summary-without-reference @@ -0,0 +1,6 @@ +# pyhegp summary file version 1 +# number-of-samples 10 +chromosome position mean standard-deviation +chr1 1 0 1 +chr2 19 2 3 +chrX 21 4 5 diff --git a/test-data/genotype-without-reference.tsv b/test-data/genotype-without-reference.tsv new file mode 100644 index 0000000..cd7cbbd --- /dev/null +++ b/test-data/genotype-without-reference.tsv @@ -0,0 +1,101 @@ +chromosome position Q_CFW-SW/100.0a Q_CFW-SW/100.0c Q_CFW-SW/100.0d Q_CFW-SW/100.0e Q_CFW-SW/100.0f Q_CFW-SW/100.0g Q_CFW-SW/100.0h Q_CFW-SW/100.0i Q_CFW-SW/100.0j Q_CFW-SW/100.0l Q_CFW-SW/100.0m Q_CFW-SW/100.0n Q_CFW-SW/100.0o Q_CFW-SW/100.0p Q_CFW-SW/100.0q Q_CFW-SW/100.0r Q_CFW-SW/10.0b Q_CFW-SW/10.0c Q_CFW-SW/10.0d Q_CFW-SW/10.0f +chr11 3200246 0.4043 0.3655 0.3375 -0.614 0.3452 0.3836 0.3901 0.2411 -0.1418 0.3629 -1.8435 0.3742 -0.5826 0.4141 -0.0555 0.2733 0.408 0.388 -3.6091 0.381 +chr11 3205355 0.395 0.3545 0.3325 -0.5421 0.3433 0.3751 0.3806 0.2034 -0.1 0.3539 -1.9966 0.3681 -0.4778 0.4084 -0.0767 0.2807 0.3991 0.384 -3.5452 0.3728 +chr11 3218908 0.3977 0.3207 0.3134 -0.4491 0.3267 0.3576 0.3449 0.1215 -0.0346 0.3294 -2.3341 0.3548 -0.2218 0.3769 -0.0873 0.3071 0.3728 0.3672 -3.5468 0.3528 +chr11 3414044 -0.3616 -0.328 -0.3234 0.074 -0.2713 -0.2976 -0.339 1.0335 -0.2665 -0.3005 3.5125 -0.3327 -0.2604 -0.3458 0.239 -0.3538 -0.3239 -0.3452 3.6101 -0.3177 +chr11 3460427 -0.341 -0.3363 -0.3346 0.073 -0.2652 -0.2791 -0.3456 1.3293 -0.2961 -0.3032 3.5493 -0.3261 -0.2861 -0.3472 0.051 -0.3419 -0.33 -0.3332 3.664 -0.3154 +chr11 3462290 -0.3552 -0.3281 -0.3287 0.0912 -0.2708 -0.2841 -0.3331 1.3928 -0.2856 -0.3056 3.5419 -0.3303 -0.2974 -0.3477 0.0408 -0.3514 -0.323 -0.343 3.6699 -0.3101 +chr11 3462323 -0.3524 -0.3296 -0.3298 0.0874 -0.2697 -0.2832 -0.3357 1.3896 -0.2873 -0.3051 3.542 -0.3294 -0.2953 -0.3476 0.0418 -0.3495 -0.3244 -0.3411 3.6675 -0.3111 +chr11 3462325 -0.3533 -0.3291 -0.3294 0.0885 -0.27 -0.2835 -0.3349 1.3909 -0.2867 -0.3052 3.5419 -0.3297 -0.296 -0.3476 0.0414 -0.3501 -0.324 -0.3417 3.6682 -0.3108 +chr11 3462348 -0.361 -0.3244 -0.326 0.0986 -0.2731 -0.2864 -0.3279 1.4031 -0.2807 -0.3064 3.541 -0.3318 -0.3018 -0.3476 0.0372 -0.3551 -0.32 -0.3469 3.6751 -0.3079 +chr11 3464016 -0.3461 -0.334 -0.3331 0.08 -0.2672 -0.2805 -0.3413 1.3757 -0.2937 -0.3044 3.543 -0.328 -0.2906 -0.3479 0.0464 -0.3455 -0.3279 -0.3369 3.6601 -0.3138 +chr11 3554197 0.3393 0.3346 0.0862 -0.1332 0.2532 0.2705 0.3409 -0.5622 0.3082 0.2896 -3.4878 0.3228 0.3214 0.3396 0.017 0.3492 0.3396 0.3289 -3.5317 0.3086 +chr11 3558414 -0.3648 -0.3172 0.0754 0.1639 -0.2644 -0.286 -0.3239 0.5833 -0.2805 -0.2923 3.3617 -0.3305 -0.342 -0.3407 -0.0391 -0.3686 -0.3297 -0.3505 3.5287 -0.2993 +chr11 3619052 -0.3394 -0.3269 1.0859 0.2534 -0.2429 -0.2508 -0.3166 0.2133 -0.3278 -0.2838 1.7148 -0.3089 -0.3337 -0.3288 -0.0442 -0.3453 -0.3142 -0.3346 2.9131 -0.2884 +chr11 3883306 -0.3207 -0.2844 2.6043 0.0664 -0.227 -0.2504 -8e-04 -0.2199 -0.3104 -0.2247 0.2938 -0.3079 -0.2412 -0.3312 -0.2698 -0.3016 -0.2836 -0.2786 -0.2529 -0.3149 +chr11 4017210 -0.3655 -0.3608 1.5442 -0.0087 -0.2506 -0.3213 0.215 -0.3742 -0.396 -0.2641 0.2322 -0.3503 -0.2296 -0.405 -0.3226 -0.3643 -0.2958 -0.3026 -0.4183 -0.3808 +chr11 4017211 -0.3685 -0.356 1.5489 -0.0107 -0.2535 -0.3241 0.2125 -0.3624 -0.3916 -0.261 0.2295 -0.3533 -0.2325 -0.4005 -0.3256 -0.3673 -0.2987 -0.3055 -0.4064 -0.3776 +chr11 4017223 -0.3824 -0.3338 1.5704 -0.02 -0.2667 -0.3373 0.2009 -0.3071 -0.3708 -0.2466 0.2171 -0.3669 -0.2459 -0.3794 -0.3394 -0.3812 -0.3125 -0.3194 -0.3509 -0.3623 +chr11 4017385 -0.3677 -0.3524 1.5514 -0.0141 -0.2529 -0.3236 0.2108 -0.3557 -0.3879 -0.2582 0.2295 -0.3526 -0.2317 -0.3968 -0.3258 -0.3665 -0.2982 -0.3048 -0.3998 -0.3746 +chr11 4022004 -0.3702 -0.3553 1.5401 -0.0114 -0.2548 -0.3259 0.2141 -0.3604 -0.3909 -0.2607 0.2282 -0.3548 -0.2332 -0.3998 -0.3266 -0.3692 -0.3 -0.307 -0.4045 -0.3774 +chr11 4024616 -0.7473 1.1971 0.937 -0.4412 -0.7211 -0.7083 -0.6358 2.9722 1.1229 0.7712 -0.7234 -0.733 -0.7373 1.1363 -0.723 -0.7502 -0.7397 -0.7496 2.9891 0.8355 +chr11 4110988 0.8081 -1.0677 -1.2622 0.66 0.7659 0.7943 0.6125 -2.8791 -1.0382 -0.985 0.6983 0.8009 0.7614 -1.0441 0.7859 0.7916 0.781 0.7821 -2.8836 -1.038 +chr11 4124677 0.8076 -0.9793 -1.1824 0.6428 0.7643 0.795 0.6135 -2.7181 -0.9575 -0.9426 0.705 0.7998 0.7611 -0.9601 0.7821 0.7882 0.78 0.7807 -2.7205 -0.9568 +chr11 4139413 -0.7222 1.0853 1.0928 -0.7139 -0.7198 -0.7216 -0.7119 2.8902 1.084 1.0653 -0.7167 -0.7218 -0.7196 1.0836 -0.721 -0.721 -0.7207 -0.7207 2.8905 1.084 +chr11 4139426 -0.717 1.0865 1.0815 -0.714 -0.7171 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4310171 0.6997 0.6996 0.6991 0.6988 0.6995 +chr11 4330042 0.7035 0.7036 0.7021 0.7013 0.703 +chr11 4908477 -0.2937 3.3684 -0.2934 -0.2937 -0.2934 +chr11 4941705 -0.2991 3.3273 -0.3012 -0.2917 -0.3011 +chr11 4944016 -0.2945 3.3274 -0.2946 -0.2944 -0.2946 +chr11 4945582 -0.2945 3.3273 -0.2946 -0.2944 -0.2946 +chr11 4949541 -0.2934 3.3271 -0.2941 -0.295 -0.294 +chr11 4971995 -0.2948 3.3243 -0.295 -0.2959 -0.295 diff --git a/test-data/genotype3-without-reference.tsv b/test-data/genotype3-without-reference.tsv new file mode 100644 index 0000000..177a626 --- /dev/null +++ b/test-data/genotype3-without-reference.tsv @@ -0,0 +1,101 @@ +chromosome position Q_CFW-SW/100.0r Q_CFW-SW/10.0b Q_CFW-SW/10.0c Q_CFW-SW/10.0d Q_CFW-SW/10.0f +chr11 3200246 0.2733 0.408 0.388 -3.6091 0.381 +chr11 3205355 0.2807 0.3991 0.384 -3.5452 0.3728 +chr11 3218908 0.3071 0.3728 0.3672 -3.5468 0.3528 +chr11 3414044 -0.3538 -0.3239 -0.3452 3.6101 -0.3177 +chr11 3460427 -0.3419 -0.33 -0.3332 3.664 -0.3154 +chr11 3462290 -0.3514 -0.323 -0.343 3.6699 -0.3101 +chr11 3462323 -0.3495 -0.3244 -0.3411 3.6675 -0.3111 +chr11 3462325 -0.3501 -0.324 -0.3417 3.6682 -0.3108 +chr11 3462348 -0.3551 -0.32 -0.3469 3.6751 -0.3079 +chr11 3464016 -0.3455 -0.3279 -0.3369 3.6601 -0.3138 +chr11 3554197 0.3492 0.3396 0.3289 -3.5317 0.3086 +chr11 3558414 -0.3686 -0.3297 -0.3505 3.5287 -0.2993 +chr11 3619052 -0.3453 -0.3142 -0.3346 2.9131 -0.2884 +chr11 3883306 -0.3016 -0.2836 -0.2786 -0.2529 -0.3149 +chr11 4017210 -0.3643 -0.2958 -0.3026 -0.4183 -0.3808 +chr11 4017211 -0.3673 -0.2987 -0.3055 -0.4064 -0.3776 +chr11 4017223 -0.3812 -0.3125 -0.3194 -0.3509 -0.3623 +chr11 4017385 -0.3665 -0.2982 -0.3048 -0.3998 -0.3746 +chr11 4022004 -0.3692 -0.3 -0.307 -0.4045 -0.3774 +chr11 4024616 -0.7502 -0.7397 -0.7496 2.9891 0.8355 +chr11 4110988 0.7916 0.781 0.7821 -2.8836 -1.038 +chr11 4124677 0.7882 0.78 0.7807 -2.7205 -0.9568 +chr11 4139413 -0.721 -0.7207 -0.7207 2.8905 1.084 +chr11 4139426 -0.7171 -0.7171 -0.7171 2.8898 1.0862 +chr11 4140742 -0.7174 -0.7174 -0.7174 2.8883 1.0853 +chr11 4141532 -0.7187 -0.7187 -0.7187 2.8742 1.0776 +chr11 4141701 -0.7173 -0.7173 -0.7173 2.8892 1.0858 +chr11 4141949 -0.7188 -0.7188 -0.7188 2.8726 1.0768 +chr11 4142088 -0.7178 -0.7178 -0.7178 2.8783 1.0802 +chr11 4142629 -0.7175 -0.7174 -0.7174 2.8877 1.085 +chr11 4142987 -0.7216 -0.7215 -0.7216 2.7988 1.0386 +chr11 4143502 -0.7177 -0.7177 -0.7177 2.8869 1.0845 +chr11 4143779 -0.7171 -0.7171 -0.7171 2.8887 1.0858 +chr11 4143838 -0.717 -0.717 -0.717 2.889 1.086 +chr11 4143850 -0.7174 -0.7174 -0.7174 2.888 1.0853 +chr11 4144873 -0.7174 -0.7174 -0.7174 2.8838 1.0832 +chr11 4146736 -0.719 -0.719 -0.7191 2.863 1.072 +chr11 4147532 -0.7188 -0.7187 -0.7187 2.8714 1.0763 +chr11 4147579 -0.7182 -0.7182 -0.7182 2.8763 1.0791 +chr11 4148004 -0.717 -0.717 -0.717 2.8874 1.0853 +chr11 4148006 -0.717 -0.717 -0.717 2.8883 1.0857 +chr11 4149618 -0.7172 -0.7172 -0.7172 2.8868 1.0848 +chr11 4151366 -0.712 -0.7119 -0.712 2.5804 0.9343 +chr11 4151391 -0.7121 -0.712 -0.7121 2.5826 0.9353 +chr11 4151936 -0.7173 -0.7173 -0.7173 2.8854 1.0841 +chr11 4156606 -0.7124 -0.7123 -0.7123 2.5788 0.9332 +chr11 4156658 -0.7125 -0.7124 -0.7124 2.5786 0.9331 +chr11 4156678 -0.7124 -0.7123 -0.7124 2.5787 0.9332 +chr11 4157061 -0.7162 -0.7163 -0.7163 2.8866 1.0854 +chr11 4157575 -0.7172 -0.7172 -0.7172 2.6516 0.9672 +chr11 4157625 -0.7124 -0.7124 -0.7124 2.5796 0.9336 +chr11 4157692 -0.7124 -0.7123 -0.7123 2.5782 0.9329 +chr11 4157786 -0.7124 -0.7123 -0.7124 2.5793 0.9334 +chr11 4157829 -0.7126 -0.7125 -0.7125 2.5807 0.9341 +chr11 4157846 -0.712 -0.7119 -0.712 2.5736 0.9308 +chr11 4158681 -0.7117 -0.7116 -0.7117 2.5688 0.9285 +chr11 4159249 -0.7176 -0.7176 -0.7176 2.883 1.0827 +chr11 4159512 -0.7124 -0.7123 -0.7124 2.5774 0.9325 +chr11 4159576 -0.7181 -0.7181 -0.7181 2.6659 0.9739 +chr11 4160767 -0.7173 -0.7173 -0.7173 2.8852 1.0839 +chr11 4161449 -0.7209 -0.7208 -0.7209 2.7387 1.0089 +chr11 4163009 -0.7123 -0.7122 -0.7122 2.5713 0.9295 +chr11 4164110 -0.7171 -0.7171 -0.7171 2.885 1.084 +chr11 4165583 -0.7191 -0.719 -0.719 2.6835 0.9822 +chr11 4166188 -0.7173 -0.7173 -0.7173 2.884 1.0833 +chr11 4169047 -0.7173 -0.7174 -0.7174 2.8676 1.0753 +chr11 4169344 -0.7172 -0.7172 -0.7172 2.8844 1.0836 +chr11 4173901 -0.7187 -0.7186 -0.7186 2.8749 1.078 +chr11 4174384 -0.7174 -0.7174 -0.7174 2.8822 1.0824 +chr11 4177048 -0.7174 -0.7174 -0.7174 2.881 1.0818 +chr11 4178320 -0.7127 -0.7127 -0.7127 2.5766 0.9319 +chr11 4178518 -0.7173 -0.7173 -0.7173 2.8834 1.083 +chr11 4183635 -0.7211 -0.7211 -0.7211 2.8293 1.0541 +chr11 4185242 -0.7173 -0.7174 -0.7174 2.8825 1.0826 +chr11 4209116 -0.7169 -0.7169 -0.7169 2.8809 1.0821 +chr11 4211694 -0.7214 -0.7214 -0.7213 2.8188 1.0487 +chr11 4228604 -0.718 -0.718 -0.718 2.8746 1.0783 +chr11 4229176 -0.7174 -0.7174 -0.7174 2.8822 1.0824 +chr11 4229195 -0.7173 -0.7173 -0.7173 2.882 1.0824 +chr11 4230918 -0.7175 -0.7175 -0.7175 2.8804 1.0815 +chr11 4237235 -0.7217 -0.7217 -0.7217 2.8039 1.0411 +chr11 4238100 -0.7218 -0.7218 -0.7217 2.8051 1.0417 +chr11 4246351 -0.7193 -0.7193 -0.7193 2.847 1.064 +chr11 4246985 -0.7218 -0.7218 -0.7217 2.8009 1.0395 +chr11 4261375 -0.7176 -0.7176 -0.7176 2.8823 1.0823 +chr11 4273327 -0.7175 -0.7175 -0.7175 2.8839 1.0832 +chr11 4283717 0.7249 0.7253 0.7249 -2.9836 -1.1298 +chr11 4284110 0.7067 0.7068 0.7067 -2.9807 -1.1376 +chr11 4285090 0.7034 0.703 0.703 -2.8865 -1.0925 +chr11 4286016 0.6996 0.6997 0.6997 -2.9627 -1.1315 +chr11 4288936 0.704 0.704 0.7041 -2.8247 -1.061 +chr11 4301371 0.6994 0.6996 0.6996 -2.964 -1.1323 +chr11 4310171 0.6997 0.6996 0.6996 -2.9604 -1.1308 +chr11 4330042 0.7035 0.7036 0.7037 -2.8725 -1.0853 +chr11 4908477 3.3681 -0.2937 -0.2934 -0.2938 -0.2937 +chr11 4941705 3.3298 -0.2983 -0.2982 -0.2917 -0.2924 +chr11 4944016 3.3274 -0.2945 -0.2945 -0.2944 -0.2944 +chr11 4945582 3.3273 -0.2945 -0.2945 -0.2944 -0.2944 +chr11 4949541 3.3267 -0.2941 -0.2944 -0.2948 -0.2948 +chr11 4971995 3.3241 -0.2952 -0.2954 -0.2958 -0.2958 diff --git a/test-data/pool-test-summary1-without-reference b/test-data/pool-test-summary1-without-reference new file mode 100644 index 0000000..5ea4287 --- /dev/null +++ b/test-data/pool-test-summary1-without-reference @@ -0,0 +1,5 @@ +# pyhegp summary file version 1 +# number-of-samples 10 +chromosome position mean standard-deviation +chr1 1 0 1 +chr2 19 2 3 diff --git a/test-data/pool-test-summary2-without-reference b/test-data/pool-test-summary2-without-reference new file mode 100644 index 0000000..e0aede0 --- /dev/null +++ b/test-data/pool-test-summary2-without-reference @@ -0,0 +1,7 @@ +# pyhegp summary file version 1 +# number-of-samples 5 +chromosome position mean standard-deviation +chr1 1 0 1 +chr2 19 2 3 +chrX 21 4 5 +chrX 21 4 5 diff --git a/tests/test_pyhegp.py b/tests/test_pyhegp.py index d119858..cdf3a7f 100644 --- a/tests/test_pyhegp.py +++ b/tests/test_pyhegp.py @@ -26,6 +26,7 @@ from hypothesis import given, strategies as st from hypothesis.extra.numpy import arrays, array_shapes import numpy as np import pandas as pd +import pytest from pytest import approx from pyhegp.pyhegp import Stats, main, hegp_encrypt, hegp_decrypt, random_key, pool_stats, standardize, unstandardize, genotype_summary, encrypt_genotype, encrypt_phenotype, cat_genotype, cat_phenotype @@ -52,12 +53,17 @@ def test_pool_stats(pools): and pooled_stats.std == approx(np.std(combined_pool, axis=0, ddof=1), rel=1e-6)) -def test_encrypt_command(tmp_path): - shutil.copy("test-data/encrypt-test-genotype.tsv", tmp_path) - ciphertext = tmp_path / "encrypt-test-genotype.tsv.hegp" +@pytest.mark.parametrize("genotype_file,summary_file", + [(Path("test-data/encrypt-test-genotype.tsv"), + Path("test-data/encrypt-test-summary")), + (Path("test-data/encrypt-test-genotype-without-reference.tsv"), + Path("test-data/encrypt-test-summary-without-reference"))]) +def test_encrypt_command(tmp_path, genotype_file, summary_file): + shutil.copy(genotype_file, tmp_path) + ciphertext = tmp_path / f"{genotype_file.name}.hegp" result = CliRunner().invoke(main, ["encrypt", - "-s", "test-data/encrypt-test-summary", - str(tmp_path / "encrypt-test-genotype.tsv")]) + "-s", summary_file, + str(tmp_path / genotype_file.name)]) assert result.exit_code == 0 assert ciphertext.exists() assert "Dropped 1 SNP(s)" in result.output @@ -143,13 +149,17 @@ def test_encrypt_genotype_does_not_produce_na(genotype, key): def test_encrypt_phenotype_does_not_produce_na(phenotype, key): assert not encrypt_phenotype(phenotype, key).isna().any(axis=None) -def test_pool_command(tmp_path): +@pytest.mark.parametrize("summary_files", + [[Path("test-data/pool-test-summary1"), + Path("test-data/pool-test-summary2")], + [Path("test-data/pool-test-summary1-without-reference"), + Path("test-data/pool-test-summary2-without-reference")]]) +def test_pool_command(tmp_path, summary_files): columns = ["chromosome", "position", "reference", "mean", "std"] complete_summary = tmp_path / "complete-summary" result = CliRunner().invoke(main, ["pool", "-o", complete_summary, - "test-data/pool-test-summary1", - "test-data/pool-test-summary2"], + *(str(summary_file) for summary_file in summary_files)], catch_exceptions=True) assert result.exit_code == 0 assert complete_summary.exists() @@ -203,21 +213,33 @@ def test_cat_phenotype(phenotypes): pd.testing.assert_frame_equal(complete_phenotype, cat_phenotype(split_phenotypes)) -def test_simple_workflow(tmp_path): - shutil.copy(f"test-data/genotype.tsv", tmp_path) - ciphertext = tmp_path / "genotype.tsv.hegp" +@pytest.mark.parametrize("genotype_file", + [Path("test-data/genotype.tsv"), + Path("test-data/genotype-without-reference.tsv")]) +def test_simple_workflow(tmp_path, genotype_file): + shutil.copy(genotype_file, tmp_path) + ciphertext = tmp_path / f"{genotype_file.name}.hegp" result = CliRunner().invoke(main, - ["encrypt", str(tmp_path / "genotype.tsv")]) + ["encrypt", str(tmp_path / genotype_file.name)]) assert result.exit_code == 0 assert ciphertext.exists() -def test_joint_workflow(tmp_path): +@pytest.mark.parametrize("genotype_files", + [[Path("test-data/genotype0.tsv"), + Path("test-data/genotype1.tsv"), + Path("test-data/genotype2.tsv"), + Path("test-data/genotype3.tsv")], + [Path("test-data/genotype0-without-reference.tsv"), + Path("test-data/genotype1-without-reference.tsv"), + Path("test-data/genotype2-without-reference.tsv"), + Path("test-data/genotype3-without-reference.tsv")]]) +def test_joint_workflow(tmp_path, genotype_files): runner = CliRunner() - for i in range(4): - shutil.copy(f"test-data/genotype{i}.tsv", tmp_path) - summary = tmp_path / f"summary{i}" + for genotype_file in genotype_files: + shutil.copy(genotype_file, tmp_path) + summary = tmp_path / f"{genotype_file.name}.summary" result = runner.invoke( - main, ["summary", str(tmp_path / f"genotype{i}.tsv"), + main, ["summary", str(tmp_path / genotype_file.name), "-o", summary]) assert result.exit_code == 0 assert summary.exists() @@ -225,21 +247,23 @@ def test_joint_workflow(tmp_path): result = runner.invoke( main, ["pool", "-o", complete_summary, - *(str(tmp_path / f"summary{i}") for i in range(4))]) + *(str(tmp_path / f"{genotype_file.name}.summary") + for genotype_file in genotype_files)]) assert result.exit_code == 0 assert complete_summary.exists() - for i in range(4): - ciphertext = tmp_path / f"genotype{i}.tsv.hegp" + for genotype_file in genotype_files: + ciphertext = tmp_path / f"{genotype_file.name}.hegp" result = runner.invoke( main, ["encrypt", "-s", complete_summary, - str(tmp_path / f"genotype{i}.tsv")]) + str(tmp_path / f"{genotype_file.name}")]) assert result.exit_code == 0 assert ciphertext.exists() complete_ciphertext = tmp_path / "complete-genotype.tsv.hegp" result = runner.invoke( main, ["cat-genotype", "-o", complete_ciphertext, - *(str(tmp_path / f"genotype{i}.tsv.hegp") for i in range(4))]) + *(str(tmp_path / f"{genotype_file.name}.hegp") + for genotype_file in genotype_files)]) assert result.exit_code == 0 assert complete_ciphertext.exists() |