diff --git a/Cargo.lock b/Cargo.lock index bf92b05..cbbbe9e 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -9,42 +9,17 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "91429305e9f0a25f6205c5b8e0d2db09e0708a7a6df0f42212bb56c32c8ac97a" dependencies = [ "cfg-if", - "getrandom", "once_cell", "version_check", "zerocopy", ] -[[package]] -name = "aho-corasick" -version = "1.1.2" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b2969dcb958b36655471fc61f7e416fa76033bdd4bfed0678d8fee1e2d07a1f0" -dependencies = [ - "memchr", -] - [[package]] name = "allocator-api2" version = "0.2.16" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "0942ffc6dcaadf03badf6e6a2d0228460359d5e34b57ccdc720b7382dfbd5ec5" -[[package]] -name = "android-tzdata" -version = "0.1.1" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e999941b234f3131b00bc13c22d06e8c5ff726d1b6318ac7eb276997bbb4fef0" - -[[package]] -name = "android_system_properties" -version = "0.1.5" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "819e7219dbd41043ac279b19830f2efc897156490d7fd6ea916720117ee66311" -dependencies = [ - "libc", -] - [[package]] name = "anstream" version = "0.6.5" @@ -99,31 +74,6 @@ version = "1.0.75" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "a4668cab20f66d8d020e1fbc0ebe47217433c1b6c8f2040faf858554e394ace6" -[[package]] -name = "argminmax" -version = "0.6.1" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "202108b46429b765ef483f8a24d5c46f48c14acfdacc086dd4ab6dddf6bcdbd2" -dependencies = [ - "num-traits", -] - -[[package]] -name = "array-init-cursor" -version = "0.2.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "bf7d0a018de4f6aa429b9d33d69edf69072b1c5b1cb8d3e4a5f7ef898fc3eb76" - -[[package]] -name = "arrow-format" -version = "0.8.1" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "07884ea216994cdc32a2d5f8274a8bee979cfe90274b83f86f440866ee3132c7" -dependencies = [ - "planus", - "serde", -] - [[package]] name = "assert_cmd" version = "2.0.12" @@ -139,21 +89,6 @@ dependencies = [ "wait-timeout", ] -[[package]] -name = "atoi" -version = "2.0.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f28d99ec8bfea296261ca1af174f24225171fea9664ba9003cbebee704810528" -dependencies = [ - "num-traits", -] - -[[package]] -name = "atoi_simd" -version = "0.15.5" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ccfc14f5c3e34de57539a7ba9c18ecde3d9bbde48d232ea1da3e468adb307fd0" - [[package]] name = "autocfg" version = "1.1.0" @@ -183,45 +118,12 @@ dependencies = [ "serde", ] -[[package]] -name = "bumpalo" -version = "3.14.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7f30e7476521f6f8af1a1c4c0b8cc94f0bee37d91763d0ca2665f299b6cd8aec" - -[[package]] -name = "bytemuck" -version = "1.14.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "374d28ec25809ee0e23827c2ab573d729e293f281dfe393500e7ad618baa61c6" -dependencies = [ - "bytemuck_derive", -] - -[[package]] -name = "bytemuck_derive" -version = "1.5.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "965ab7eb5f8f97d2a083c799f3a1b994fc397b2fe2da5d1da1626ce15a39f2b1" -dependencies = [ - "proc-macro2", - "quote", - "syn 2.0.41", -] - -[[package]] -name = "bytes" -version = "1.5.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a2bd12c1caf447e69cd4528f47f94d203fd2582878ecb9e9465484c4148a8223" - [[package]] name = "cc" version = "1.0.83" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "f1174fb0b6ec23863f8b971027804a42614e347eafb0a95bf0b12cdae21fc4d0" dependencies = [ - "jobserver", "libc", ] @@ -231,18 +133,6 @@ version = "1.0.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd" -[[package]] -name = "chrono" -version = "0.4.31" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7f2c685bad3eb3d45a01354cedb7d5faa66194d1d58ba6e267a8de788f79db38" -dependencies = [ - "android-tzdata", - "iana-time-zone", - "num-traits", - "windows-targets 0.48.5", -] - [[package]] name = "clap" version = "4.4.11" @@ -277,7 +167,7 @@ dependencies = [ "heck", "proc-macro2", "quote", - "syn 2.0.41", + "syn", ] [[package]] @@ -292,18 +182,6 @@ version = "1.0.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "acbf1af155f9b9ef647e42cdc158db4b64a1b61f743629225fde6f3e0be2a7c7" -[[package]] -name = "comfy-table" -version = "7.1.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7c64043d6c7b7a4c58e39e7efccfdea7b93d885a795d0c054a69dbbf4dd52686" -dependencies = [ - "crossterm", - "strum", - "strum_macros", - "unicode-width", -] - [[package]] name = "console" version = "0.15.7" @@ -317,12 +195,6 @@ dependencies = [ "windows-sys 0.45.0", ] -[[package]] -name = "core-foundation-sys" -version = "0.8.6" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "06ea2b9bc92be3c2baa9334a323ebca2d6f074ff852cd1d7b11064035cd3868f" - [[package]] name = "crossbeam-channel" version = "0.5.9" @@ -356,16 +228,6 @@ dependencies = [ "memoffset", ] -[[package]] -name = "crossbeam-queue" -version = "0.3.9" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b9bcf5bdbfdd6030fb4a1c497b5d5fc5921aa2f60d359a17e249c0e6df3de153" -dependencies = [ - "cfg-if", - "crossbeam-utils", -] - [[package]] name = "crossbeam-utils" version = "0.8.17" @@ -375,28 +237,6 @@ dependencies = [ "cfg-if", ] -[[package]] -name = "crossterm" -version = "0.27.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f476fe445d41c9e991fd07515a6f463074b782242ccf4a5b7b1d1012e70824df" -dependencies = [ - "bitflags 2.4.1", - "crossterm_winapi", - "libc", - "parking_lot", - "winapi", -] - -[[package]] -name = "crossterm_winapi" -version = "0.9.1" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "acdd7c62a3665c7f6830a51635d9ac9b23ed385797f70a83bb8bafe9c572ab2b" -dependencies = [ - "winapi", -] - [[package]] name = "csv" version = "1.3.0" @@ -430,12 +270,6 @@ version = "0.3.3" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "fea41bba32d969b513997752735605054bc0dfa92b4c56bf1189f2e174be7a10" -[[package]] -name = "dyn-clone" -version = "1.0.16" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "545b22097d44f8a9581187cdf93de7a71e4722bf51200cfaba810865b49a495d" - [[package]] name = "either" version = "1.9.0" @@ -448,24 +282,6 @@ version = "0.3.6" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "a357d28ed41a50f9c765dbfe56cbc04a64e53e5fc58ba79fbc34c10ef3df831f" -[[package]] -name = "enum_dispatch" -version = "0.3.12" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8f33313078bb8d4d05a2733a94ac4c2d8a0df9a2b84424ebf4f33bfc224a890e" -dependencies = [ - "once_cell", - "proc-macro2", - "quote", - "syn 2.0.41", -] - -[[package]] -name = "equivalent" -version = "1.0.1" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "5443807d6dff69373d433ab9ef5378ad8df50ca6298caf15de6e52e24aaf54d5" - [[package]] name = "errno" version = "0.3.8" @@ -476,12 +292,6 @@ dependencies = [ "windows-sys 0.52.0", ] -[[package]] -name = "ethnum" -version = "1.5.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b90ca2580b73ab6a1f724b76ca11ab632df820fd6040c336200d2c1df7b3c82c" - [[package]] name = "fallible-iterator" version = "0.3.0" @@ -494,24 +304,12 @@ version = "0.1.9" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "7360491ce676a36bf9bb3c56c1aa791658183a54d2744120f27285738d90465a" -[[package]] -name = "fast-float" -version = "0.2.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "95765f67b4b18863968b4a1bd5bb576f732b29a4a28c7cd84c09fa3e2875f33c" - [[package]] name = "fastrand" version = "2.0.1" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "25cbce373ec4653f1a01a31e8a5e5ec0c622dc27ff9c4e6606eefef5cbbed4a5" -[[package]] -name = "foreign_vec" -version = "0.1.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ee1b05cbd864bcaecbd3455d6d967862d446e4ebfc3c2e5e5b9841e53cba6673" - [[package]] name = "futures" version = "0.3.29" @@ -568,7 +366,7 @@ checksum = "53b153fd91e4b0147f4aced87be237c98248656bb01050b96bf3ee89220a8ddb" dependencies = [ "proc-macro2", "quote", - "syn 2.0.41", + "syn", ] [[package]] @@ -601,19 +399,6 @@ dependencies = [ "slab", ] -[[package]] -name = "getrandom" -version = "0.2.11" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "fe9006bed769170c11f845cf00c7c1e9092aeb3f268e007c3e760ac68008070f" -dependencies = [ - "cfg-if", - "js-sys", - "libc", - "wasi", - "wasm-bindgen", -] - [[package]] name = "glob" version = "0.3.1" @@ -628,7 +413,6 @@ checksum = "290f1a1d9242c78d09ce40a5e87e7554ee637af1351968159f4952f028f75604" dependencies = [ "ahash", "allocator-api2", - "rayon", ] [[package]] @@ -652,48 +436,6 @@ version = "0.3.3" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "d77f7ec81a6d05a3abb01ab6eb7590f6083d08449fe5a1c8b1e620283546ccb7" -[[package]] -name = "home" -version = "0.5.9" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e3d1354bf6b7235cb4a0576c2619fd4ed18183f689b12b006a0ee7329eeff9a5" -dependencies = [ - "windows-sys 0.52.0", -] - -[[package]] -name = "iana-time-zone" -version = "0.1.58" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8326b86b6cff230b97d0d312a6c40a60726df3332e721f72a1b035f451663b20" -dependencies = [ - "android_system_properties", - "core-foundation-sys", - "iana-time-zone-haiku", - "js-sys", - "wasm-bindgen", - "windows-core", -] - -[[package]] -name = "iana-time-zone-haiku" -version = "0.1.2" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f31827a206f56af32e590ba56d5d2d085f558508192593743f16b2306495269f" -dependencies = [ - "cc", -] - -[[package]] -name = "indexmap" -version = "2.1.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d530e1a18b1cb4c484e6e34556a0d948706958449fca0cab753d649f2bce3d1f" -dependencies = [ - "equivalent", - "hashbrown", -] - [[package]] name = "indicatif" version = "0.17.7" @@ -741,24 +483,6 @@ version = "1.0.10" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "b1a46d1a171d865aa5f83f92695765caa047a9b4cbae2cbf37dbd613a793fd4c" -[[package]] -name = "jobserver" -version = "0.1.27" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8c37f63953c4c63420ed5fd3d6d398c719489b9f872b9fa683262f8edd363c7d" -dependencies = [ - "libc", -] - -[[package]] -name = "js-sys" -version = "0.3.66" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "cee9c64da59eae3b50095c18d3e74f8b73c0b86d2792824ff01bbce68ba229ca" -dependencies = [ - "wasm-bindgen", -] - [[package]] name = "lazy_static" version = "1.4.0" @@ -771,12 +495,6 @@ version = "0.2.151" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "302d7ab3130588088d277783b1e2d2e10c9e9e4a16dd9050e6ec93fb3e7048f4" -[[package]] -name = "libm" -version = "0.2.8" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4ec2a862134d2a7d32d7983ddcdd1c4923530833c9f2ea1a44fc5fa473989058" - [[package]] name = "libsqlite3-sys" version = "0.27.0" @@ -793,42 +511,6 @@ version = "0.4.12" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "c4cd1a83af159aa67994778be9070f0ae1bd732942279cabb14f86f986a21456" -[[package]] -name = "lock_api" -version = "0.4.11" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "3c168f8615b12bc01f9c17e2eb0cc07dcae1940121185446edc3744920e8ef45" -dependencies = [ - "autocfg", - "scopeguard", -] - -[[package]] -name = "log" -version = "0.4.20" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b5e6163cb8c49088c2c36f57875e58ccd8c87c7427f7fbd50ea6710b2f3f2e8f" - -[[package]] -name = "lz4" -version = "1.24.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7e9e2dd86df36ce760a60f6ff6ad526f7ba1f14ba0356f8254fb6905e6494df1" -dependencies = [ - "libc", - "lz4-sys", -] - -[[package]] -name = "lz4-sys" -version = "1.9.4" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "57d27b317e207b10f69f5e75494119e391a96f48861ae870d1da6edac98ca900" -dependencies = [ - "cc", - "libc", -] - [[package]] name = "matrixmultiply" version = "0.3.8" @@ -845,15 +527,6 @@ version = "2.6.4" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "f665ee40bc4a3c5590afb1e9677db74a508659dfd71e126420da8274909a0167" -[[package]] -name = "memmap2" -version = "0.7.1" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f49388d20533534cd19360ad3d6a7dadc885944aa802ba3995040c5ec11288c6" -dependencies = [ - "libc", -] - [[package]] name = "memoffset" version = "0.9.0" @@ -863,28 +536,6 @@ dependencies = [ "autocfg", ] -[[package]] -name = "multiversion" -version = "0.7.3" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b2c7b9d7fe61760ce5ea19532ead98541f6b4c495d87247aff9826445cf6872a" -dependencies = [ - "multiversion-macros", - "target-features", -] - -[[package]] -name = "multiversion-macros" -version = "0.7.3" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "26a83d8500ed06d68877e9de1dde76c1dbb83885dcdbda4ef44ccbc3fbda2ac8" -dependencies = [ - "proc-macro2", - "quote", - "syn 1.0.109", - "target-features", -] - [[package]] name = "ndarray" version = "0.15.6" @@ -898,24 +549,6 @@ dependencies = [ "rawpointer", ] -[[package]] -name = "now" -version = "0.1.3" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "6d89e9874397a1f0a52fc1f197a8effd9735223cb2390e9dcc83ac6cd02923d0" -dependencies = [ - "chrono", -] - 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-[[package]] -name = "winapi-x86_64-pc-windows-gnu" -version = "0.4.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f" - -[[package]] -name = "windows-core" -version = "0.51.1" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f1f8cf84f35d2db49a46868f947758c7a1138116f7fac3bc844f43ade1292e64" -dependencies = [ - "windows-targets 0.48.5", -] - [[package]] name = "windows-sys" version = "0.45.0" @@ -2101,12 +1103,6 @@ version = "0.52.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "dff9641d1cd4be8d1a070daf9e3773c5f67e78b4d9d42263020c057706765c04" -[[package]] -name = "xxhash-rust" -version = "0.8.7" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "9828b178da53440fa9c766a3d2f73f7cf5d0ac1fe3980c1e5018d899fd19e07b" - [[package]] name = "zerocopy" version = "0.7.31" @@ -2124,33 +1120,5 @@ checksum = "b3c129550b3e6de3fd0ba67ba5c81818f9805e58b8d7fee80a3a59d2c9fc601a" dependencies = [ "proc-macro2", "quote", - "syn 2.0.41", -] - -[[package]] -name = "zstd" -version = "0.13.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "bffb3309596d527cfcba7dfc6ed6052f1d39dfbd7c867aa2e865e4a449c10110" -dependencies = [ - "zstd-safe", -] - -[[package]] -name = "zstd-safe" -version = "7.0.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "43747c7422e2924c11144d5229878b98180ef8b06cca4ab5af37afc8a8d8ea3e" -dependencies = [ - "zstd-sys", -] - -[[package]] -name = "zstd-sys" -version = "2.0.9+zstd.1.5.5" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "9e16efa8a874a0481a574084d34cc26fdb3b99627480f785888deb6386506656" -dependencies = [ - "cc", - "pkg-config", + "syn", ] diff --git a/Cargo.toml b/Cargo.toml index 2e2e9de..77d341b 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -16,9 +16,9 @@ indicatif = { version = "0.17.7", features = ["rayon"] } itertools = "0.12.0" ndarray = "0.15.6" num_cpus = "1.16.0" -polars = { version = "0.35.4", features = ["lazy", "ndarray", "performant", "sign"] } +rayon = "1.8.1" rusqlite = "0.30.0" -serde = "1.0.193" +serde = {version = "1.0.193", features = ["derive"]} serde_rusqlite = "0.34.0" tempfile = "3.9.0" diff --git a/src/align.rs b/src/align.rs new file mode 100644 index 0000000..32ab0d3 --- /dev/null +++ b/src/align.rs @@ -0,0 +1,114 @@ +use std::collections::HashMap; + +use crate::io::gwas::{GwasLine, GwasSumstats}; +use crate::io::tagging::{TagInfo, TagLine}; + +pub fn check_aligned(gwas: &GwasSumstats, taginfo: &TagInfo) -> bool { + gwas.predictors == taginfo.predictors +} + +pub fn align_gwas_taginfo(gwas: &GwasSumstats, taginfo: &TagInfo) -> (GwasSumstats, TagInfo) { + let gwas_predictor_to_idx: HashMap = gwas + .results + .iter() + .enumerate() + .map(|(i, x)| (x.predictor.clone(), i)) + .collect(); + + let tag_predictor_to_idx: HashMap = taginfo + .taglines + .iter() + .enumerate() + .map(|(i, x)| (x.predictor.clone(), i)) + .collect(); + + let common_predictors: Vec = taginfo + .predictors + .clone() + .into_iter() + .filter(|x| gwas_predictor_to_idx.contains_key(x)) + .collect(); + + let gwas_results: Vec = common_predictors + .iter() + .map(|x| gwas_predictor_to_idx[x]) + .map(|x| gwas.results[x].clone()) + .collect(); + + let taginfo_taglines: Vec = common_predictors + .iter() + .map(|x| tag_predictor_to_idx[x]) + .map(|x| taginfo.taglines[x].clone()) + .collect(); + + ( + GwasSumstats::new(gwas.phenotype.clone(), gwas_results), + TagInfo::new( + taginfo_taglines, + taginfo.annotation_names.clone(), + taginfo.ssums.clone(), + ), + ) +} + +pub fn align_gwas_gwas( + left: &GwasSumstats, + right: &GwasSumstats, + taginfo: &TagInfo, +) -> (GwasSumstats, GwasSumstats, TagInfo) { + let left_predictor_to_idx: HashMap = left + .results + .iter() + .enumerate() + .map(|(i, x)| (x.predictor.clone(), i)) + .collect(); + + let right_predictor_to_idx: HashMap = right + .results + .iter() + .enumerate() + .map(|(i, x)| (x.predictor.clone(), i)) + .collect(); + + let tag_predictor_to_idx: HashMap = taginfo + .taglines + .iter() + .enumerate() + .map(|(i, x)| (x.predictor.clone(), i)) + .collect(); + + let common_predictors: Vec = left + .predictors + .clone() + .into_iter() + .filter(|x| right_predictor_to_idx.contains_key(x) && tag_predictor_to_idx.contains_key(x)) + .collect(); + + let left_results: Vec = common_predictors + .iter() + .map(|x| left_predictor_to_idx[x]) + .map(|x| left.results[x].clone()) + .collect(); + + let right_results: Vec = common_predictors + .iter() + .map(|x| right_predictor_to_idx[x]) + .map(|x| right.results[x].clone()) + .collect(); + + let taginfo_taglines: Vec = common_predictors + .iter() + .map(|x| tag_predictor_to_idx[x]) + .map(|x| taginfo.taglines[x].clone()) + .collect(); + + ( + GwasSumstats::new(left.phenotype.clone(), left_results), + GwasSumstats::new(right.phenotype.clone(), right_results), + TagInfo::new( + taginfo_taglines, + taginfo.annotation_names.clone(), + taginfo.ssums.clone(), + ), + ) +} diff --git a/src/db.rs b/src/db.rs index bcca7c7..3bc2b75 100644 --- a/src/db.rs +++ b/src/db.rs @@ -4,7 +4,8 @@ use serde_rusqlite::to_params_named; use std::collections::HashSet; use std::path::Path; -use crate::hsq::{HsqResult, RgResult}; +use crate::hsq::HsqResult; +use crate::rg::RgResult; pub struct DbConnection { pub conn: Connection, @@ -91,7 +92,7 @@ impl DbConnection { fn insert_hsq_data(tx: &Transaction, rows: &[HsqResult]) -> Result<()> { let mut stmt = tx.prepare_cached( - "INSERT INTO h2 (phenotype, component, estimate, std_error) VALUES + "INSERT INTO h2 (phenotype, component, estimate, std_error) VALUES (:phenotype, :component, :estimate, :se)", )?; @@ -105,7 +106,7 @@ fn insert_hsq_data(tx: &Transaction, rows: &[HsqResult]) -> Result<()> { fn insert_rg_data(tx: &Transaction, rows: &[RgResult]) -> Result<()> { let mut stmt = tx.prepare_cached( - "INSERT INTO rg (phenotype1, phenotype2, component, estimate, std_error) VALUES + "INSERT INTO rg (phenotype1, phenotype2, component, estimate, std_error) VALUES (:phenotype1, :phenotype2, :component, :estimate, :se)", )?; diff --git a/src/ffi.rs b/src/ffi.rs index 6d5f760..e018ed6 100644 --- a/src/ffi.rs +++ b/src/ffi.rs @@ -1,4 +1,4 @@ -use crate::io::gwas::AlignedGwasSumstats; +use crate::io::gwas::GwasSumstats; use anyhow::{anyhow, Result}; @@ -165,8 +165,8 @@ pub fn solve_sums_wrapper( pub fn solve_cors_wrapper( tagging: &[f64], - gwas_sumstats_1: &AlignedGwasSumstats, - gwas_sumstats_2: &AlignedGwasSumstats, + gwas_sumstats_1: &GwasSumstats, + gwas_sumstats_2: &GwasSumstats, category_vals: &[Vec], category_contribs: &[Vec], options: Option, @@ -192,10 +192,10 @@ pub fn solve_cors_wrapper( tagging.as_ptr(), svars.as_ptr(), ssums.as_ptr(), - gwas_sumstats_1.sample_sizes.as_ptr(), + gwas_sumstats_1.sample_size.as_ptr(), gwas_sumstats_1.chisq.as_ptr(), gwas_sumstats_1.rhos.as_ptr(), - gwas_sumstats_2.sample_sizes.as_ptr(), + gwas_sumstats_2.sample_size.as_ptr(), gwas_sumstats_2.chisq.as_ptr(), gwas_sumstats_2.rhos.as_ptr(), options.as_ref().and_then(|x| x.tol).unwrap_or(0.0001), @@ -213,3 +213,87 @@ pub fn solve_cors_wrapper( cept, }) } + +#[cfg(test)] +mod tests { + use super::*; + + #[test] + fn test_solve_sums_wrapper() { + let tagging = vec![1.0, 2.0, 3.0]; + let chisqs = vec![1.0, 2.0, 3.0]; + let sample_sizes = vec![1.0, 2.0, 3.0]; + let category_vals = vec![vec![1.0, 2.0, 3.0], vec![4.0, 5.0, 6.0]]; + let category_contribs = vec![vec![1.0, 2.0, 3.0], vec![4.0, 5.0, 6.0]]; + + let result = solve_sums_wrapper( + &tagging, + &chisqs, + &sample_sizes, + &category_vals, + &category_contribs, + None, + ) + .unwrap(); + + // Check sizes + assert_eq!(result.stats.len(), 3 * (2 + 1 + 2)); + assert_eq!(result.likes.len(), 11); + assert_eq!(result.cohers.len(), 2 * 2); + assert_eq!(result.influs.len(), 2); + + // Check values + let desired_stats = [ + 0.4791464197764975, + -0.5588545017977516, + -0.07970808202125412, + 0.2556046190573969, + 1.3577311773082386, + 2.3675053949121336, + 4.497316861083112, + 2.2773633495918704, + 0.763803940571641, + 5.227708866852336, + 146.47111303693012, + 146.47111303693012, + 0.0, + 87.88266782215808, + 439.41333911079033, + ]; + for (i, &x) in result.stats.iter().enumerate() { + assert!((x - desired_stats[i]).abs() < 1e-10); + } + + let desired_likes = [ + -3.5411094874599045, + -3.3166019866559435, + -2.601387310875233, + 0.6760515111840476, + -0.8075528916021616, + 1.0601008469882118, + 1.0, + 0.0, + 0.0, + 0.0, + 0.0, + ]; + for (i, &x) in result.likes.iter().enumerate() { + assert!((x - desired_likes[i]).abs() < 1e-10); + } + + let desired_cohers = [ + 5.605081794938058, + -10.322278458928105, + -10.322278458928107, + 20.22585894898246, + ]; + for (i, &x) in result.cohers.iter().enumerate() { + assert!((x - desired_cohers[i]).abs() < 1e-10); + } + + let desired_influs = [4.363636363636364, 1.8545454545454547]; + for (i, &x) in result.influs.iter().enumerate() { + assert!((x - desired_influs[i]).abs() < 1e-10); + } + } +} diff --git a/src/hsq.rs b/src/hsq.rs index 1599bb1..f2fa006 100644 --- a/src/hsq.rs +++ b/src/hsq.rs @@ -1,40 +1,97 @@ -use std::path::{Path, PathBuf}; -use std::sync::{Arc, Mutex}; +use std::path::Path; +use std::path::PathBuf; + +use anyhow::Result; +use itertools::Itertools; +use rayon::prelude::*; +use serde::Serialize; + +use crate::align::{align_gwas_taginfo, check_aligned}; +use crate::db::Progress; +use crate::ffi::{solve_sums_wrapper, SolveSumsResult}; +use crate::io::common::round_serialize; +use crate::io::gwas::GwasSumstats; +use crate::io::tagging::TagInfo; +use crate::util::{make_progressbar, RuntimeSetup}; + +pub fn compute_h2

( + tag_path: P, + gwas_paths: &[PathBuf], + runtime_setup: &RuntimeSetup, +) -> Result<()> +where + P: AsRef, +{ + let gwas_paths = remove_computed_h2(gwas_paths, &runtime_setup.computed); + if gwas_paths.is_empty() { + return Ok(()); + } + let tag_info = TagInfo::from_file(tag_path)?; + let pb = make_progressbar(gwas_paths.len() as u64); -use crate::db::{DbConnection, Progress}; -use crate::ffi::{solve_cors_wrapper, solve_sums_wrapper, SolveCorsResult, SolveSumsResult}; -use crate::io::gwas::{sumstat_processor, sumstat_reader, AlignedGwasSumstats, RawGwasSumstats}; -use crate::io::tagging::{read_tagfile, TagInfo}; -use crate::util::{align_if_possible, check_predictors_aligned, make_progressbar, RuntimeSetup}; + for chunk in gwas_paths + .iter() + .chunks(runtime_setup.chunk_size) + .into_iter() + { + let results = chunk + .collect::>() + .par_iter() + .map(|x| { + let mut gwas = GwasSumstats::from_file(x)?; // TODO: error handling after pb + let res = wrap_h2(&mut tag_info.clone(), &mut gwas); + pb.lock().unwrap().inc(1); + res + }) + .collect::>>()? + .into_iter() + .flatten() + .collect::>(); + + runtime_setup.db_conn.lock().unwrap().write_h2(&results)?; + } -use anyhow::{anyhow, Context, Result}; -use crossbeam_channel::{Receiver, Sender}; -use indicatif::ProgressBar; -use serde::{Serialize, Serializer}; + Ok(()) +} -fn round_serialize(x: &f64, s: S) -> Result -where - S: Serializer, -{ - s.serialize_str(&format!("{:.6}", x)) +fn remove_computed_h2(gwas_paths: &[PathBuf], computed: &Progress) -> Vec { + gwas_paths + .iter() + .filter(|x| { + !computed + .finished_h2 + .contains(x.file_name().unwrap().to_str().unwrap()) + }) + .cloned() + .collect() } -#[derive(Debug, Serialize)] -pub struct HsqResult { - pub phenotype: String, - pub component: String, +fn wrap_h2(tag_info: &mut TagInfo, gwas_sumstats: &mut GwasSumstats) -> Result> { + if !check_aligned(gwas_sumstats, tag_info) { + (*gwas_sumstats, *tag_info) = align_gwas_taginfo(gwas_sumstats, tag_info); + } - #[serde(serialize_with = "round_serialize")] - pub estimate: f64, + let result = solve_sums_wrapper( + &tag_info.tagging, + &gwas_sumstats.chisq, + &gwas_sumstats.sample_size, + &tag_info.annotations, + &tag_info.ssums, + None, + )?; - #[serde(serialize_with = "round_serialize")] - pub se: f64, + let h2_results = format_heritability( + &gwas_sumstats.phenotype, + &result, + &tag_info.annotation_names, + ); + + Ok(h2_results) } #[derive(Debug, Serialize)] -pub struct RgResult { - pub phenotype1: String, - pub phenotype2: String, +pub struct HsqResult { + pub phenotype: String, pub component: String, #[serde(serialize_with = "round_serialize")] @@ -73,439 +130,3 @@ fn format_heritability( partitions } - -fn format_genetic_correlation( - phenotype1: String, - phenotype2: String, - result: &SolveCorsResult, -) -> Vec { - let num_parts = result.num_parts as usize; - let total = 2 * (result.gcon + result.cept) as usize + 3 * num_parts + 1; - let total2 = num_parts + (result.gcon + result.cept) as usize; - let se_idx = 2 * total + 4 + num_parts; - - let mut partitions = vec![ - RgResult { - phenotype1: phenotype1.clone(), - phenotype2: phenotype2.clone(), - component: "Her1_All".to_string(), - estimate: result.stats[total], - se: result.stats[se_idx], - }, - RgResult { - phenotype1: phenotype1.clone(), - phenotype2: phenotype2.clone(), - component: "Her2_All".to_string(), - estimate: result.stats[total + 1], - se: result.stats[se_idx + 1], - }, - RgResult { - phenotype1: phenotype1.clone(), - phenotype2: phenotype2.clone(), - component: "Coher_All".to_string(), - estimate: result.stats[total + 2], - se: result.stats[se_idx + 2], - }, - RgResult { - phenotype1: phenotype1.clone(), - phenotype2: phenotype2.clone(), - component: "Cor_All".to_string(), - estimate: result.stats[total + 3], - se: result.stats[se_idx + 3], - }, - ]; - - if result.gcon == 1 { - partitions.push(RgResult { - phenotype1: phenotype1.clone(), - phenotype2: phenotype2.clone(), - component: "Scaling1".to_string(), - estimate: result.stats[num_parts], - se: result.stats[2 * num_parts + 4 + total], - }); - partitions.push(RgResult { - phenotype1: phenotype1.clone(), - phenotype2: phenotype2.clone(), - component: "Scaling2".to_string(), - estimate: result.stats[total2 + num_parts], - se: result.stats[2 * num_parts + 4 + total + total2], - }); - } - - partitions.push(RgResult { - phenotype1: phenotype1.clone(), - phenotype2: phenotype2.clone(), - component: "Overlap".to_string(), - estimate: result.stats[2 * total2 + num_parts], - se: result.stats[2 * num_parts + 4 + total + 2 * total2], - }); - - partitions -} - -fn h2_result_writer( - receiver: &Receiver, - progress: &Arc>, - conn: &Mutex, -) -> Result<()> { - let mut cache = Vec::new(); - - for partition in receiver { - cache.push(partition); - - if cache.len() >= 10 { - conn.lock().unwrap().write_h2(&cache)?; - - for partition in cache.iter() { - if partition.component == "Her_All" { - progress.lock().unwrap().inc(1); - } - } - - cache.clear(); - } - } - conn.lock().unwrap().write_h2(&cache)?; - for partition in cache.iter() { - if partition.component == "Her_All" { - progress.lock().unwrap().inc(1); - } - } - - Ok(()) -} - -fn rg_result_writer( - receiver: &Receiver, - progress: &Arc>, - conn: &Mutex, -) -> Result<()> { - let mut cache = Vec::new(); - - for partition in receiver { - cache.push(partition); - - if cache.len() >= 50 { - conn.lock().unwrap().write_rg(&cache)?; - - for partition in cache.iter() { - if partition.component == "Cor_All" { - progress.lock().unwrap().inc(1); - } - } - cache.clear(); - } - } - conn.lock().unwrap().write_rg(&cache)?; - for partition in cache.iter() { - if partition.component == "Cor_All" { - progress.lock().unwrap().inc(1); - } - } - - Ok(()) -} - -fn remove_computed_h2(gwas_paths: &[PathBuf], computed: &Progress) -> Vec { - gwas_paths - .iter() - .filter(|x| !computed.finished_h2.contains(x.to_str().unwrap())) - .cloned() - .collect() -} - -pub fn compute_h2( - tag_path: &Path, - gwas_paths: &[PathBuf], - runtime_setup: &RuntimeSetup, -) -> Result<()> { - let n_original = gwas_paths.len() as u64; - let pb = make_progressbar(n_original); - let gwas_paths = remove_computed_h2(gwas_paths, &runtime_setup.computed); - pb.lock().unwrap().inc(n_original - gwas_paths.len() as u64); - if gwas_paths.is_empty() { - return Ok(()); - } - - let alignment_info = check_predictors_aligned(&gwas_paths, runtime_setup.skip_alignment_check)?; - let mut tag_info = read_tagfile(tag_path.to_str().unwrap())?; - let aligned = align_if_possible(&mut tag_info, alignment_info)?; - if !aligned { - return Err(anyhow!("GWAS summary files are not aligned!")); - } - let tag_info = Arc::new(tag_info); - - let chunks = gwas_paths - .chunks(runtime_setup.chunk_size) - .collect::>(); - - let (h2_sender, h2_receiver) = crossbeam_channel::unbounded::(); - let conn = runtime_setup.db_conn.clone(); - let writer_process = { - let h2_receiver = h2_receiver.clone(); - std::thread::spawn(move || h2_result_writer(&h2_receiver, &pb, &conn)) - }; - - for chunk in chunks.iter() { - let (sender, receiver) = crossbeam_channel::unbounded::(); - - let mut ldak_workers = Vec::new(); - for _ in 0..runtime_setup.n_threads { - let tag_info = tag_info.clone(); - let receiver = receiver.clone(); - let h2_sender = h2_sender.clone(); - ldak_workers.push(std::thread::spawn(move || { - h2_processor(&receiver, &tag_info, &h2_sender) - })); - } - - load_phenotypes_channel(chunk, &tag_info, runtime_setup, sender)?; - - for worker in ldak_workers { - worker.join().unwrap()?; - } - } - drop(h2_sender); - writer_process.join().unwrap()?; - - Ok(()) -} - -fn h2_processor( - sumstat_receiver: &Receiver, - tag_info: &TagInfo, - result_sender: &Sender, -) -> Result<()> { - let names = &tag_info.category_info.names; - - for sumstats in sumstat_receiver { - let result = solve_sums_wrapper( - &tag_info.tag_vec, - &sumstats.chisq, - &sumstats.sample_sizes, - &tag_info.cat_vec, - &tag_info.category_info.ssums, - None, - )?; - let partitions = format_heritability(&sumstats.phenotype, &result, names); - for partition in partitions { - result_sender - .send(partition) - .with_context(|| format!("Error sending h2 result for {}", &sumstats.phenotype))?; - } - } - - Ok(()) -} - -fn load_phenotypes_channel( - gwas_paths: &[PathBuf], - tag_info: &Arc, - runtime_setup: &RuntimeSetup, - output: Sender, -) -> Result<()> { - let predictor_order = Arc::new(tag_info.predictor_order.clone()); - - let mut sumstat_workers = Vec::new(); - - let (raw_sender, raw_receiver) = crossbeam_channel::unbounded::(); - - let gwas_paths = Arc::new(gwas_paths.to_vec()); - let reader_process = std::thread::spawn(move || sumstat_reader(&gwas_paths, &raw_sender)); - - for _ in 0..runtime_setup.n_threads { - let predictor_order = predictor_order.clone(); - let raw_receiver = raw_receiver.clone(); - let output = output.clone(); - sumstat_workers.push(std::thread::spawn(move || { - sumstat_processor(&predictor_order, &raw_receiver, &output) - })); - } - - reader_process.join().unwrap()?; - - for worker in sumstat_workers { - worker.join().unwrap()?; - } - drop(output); - - Ok(()) -} - -fn load_phenotypes_chunk( - gwas_paths: &[PathBuf], - tag_info: &Arc, - runtime_setup: &RuntimeSetup, -) -> Result>> { - let (aligned_sender, aligned_receiver) = crossbeam_channel::unbounded::(); - - load_phenotypes_channel(gwas_paths, tag_info, runtime_setup, aligned_sender)?; - - let mut sumstats = Vec::new(); - while let Ok(sumstat) = aligned_receiver.recv() { - sumstats.push(Arc::new(sumstat)); - } - - Ok(sumstats) -} - -fn compute_rg_chunk( - left_chunk: &[Arc], - right_chunk: &[Arc], - only_upper_tri: bool, - result_sender: &Sender, - tag_info: &Arc, - progress: &Arc>, - runtime_setup: &RuntimeSetup, -) -> Result<()> { - let (sender, receiver) = - crossbeam_channel::unbounded::<(Arc, Arc)>(); - - // Put all combinations into the channel - for (i, left) in left_chunk.iter().enumerate() { - for (j, right) in right_chunk.iter().enumerate() { - if i >= j && only_upper_tri { - continue; - } - sender.send((left.clone(), right.clone()))?; - } - } - drop(sender); - - let mut ldak_workers = Vec::new(); - for _ in 0..runtime_setup.n_threads { - let tag_info = tag_info.clone(); - let receiver = receiver.clone(); - let result_sender = result_sender.clone(); - let computed = runtime_setup.computed.clone(); - let pb = progress.clone(); - ldak_workers.push(std::thread::spawn(move || { - rg_processor(&receiver, &tag_info, &result_sender, &computed, &pb) - })); - } - - for worker in ldak_workers { - worker.join().unwrap()?; - } - - Ok(()) -} - -fn rg_pre_computed(phenotype1: &str, phenotype2: &str, computed: &Progress) -> bool { - computed - .finished_rg - .contains(&(phenotype1.to_string(), phenotype2.to_string())) - || computed - .finished_rg - .contains(&(phenotype2.to_string(), phenotype1.to_string())) -} - -fn rg_processor( - receiver: &Receiver<(Arc, Arc)>, - tag_info: &Arc, - result_sender: &Sender, - precomputed: &Progress, - progress: &Arc>, -) -> Result<()> { - for (left, right) in receiver { - if rg_pre_computed(&left.phenotype, &right.phenotype, precomputed) { - progress.lock().unwrap().inc(1); - continue; - } - - let result = solve_cors_wrapper( - &tag_info.tag_vec, - &left, - &right, - &tag_info.cat_vec, - &tag_info.category_info.ssums, - None, - ); - match result { - Ok(result) => { - let partitions = format_genetic_correlation( - left.phenotype.clone(), - right.phenotype.clone(), - &result, - ); - - for partition in partitions { - result_sender.send(partition)?; - } - } - Err(e) => { - println!( - "Error computing rg for {} and {}: {}", - left.phenotype, right.phenotype, e - ); - } - } - } - - Ok(()) -} - -pub fn compute_rg( - tag_path: &Path, - gwas_paths: &[PathBuf], - runtime_setup: &RuntimeSetup, -) -> Result<()> { - let mut tag_info = read_tagfile(tag_path.to_str().unwrap())?; - let alignment_info = check_predictors_aligned(gwas_paths, runtime_setup.skip_alignment_check)?; - let aligned = align_if_possible(&mut tag_info, alignment_info)?; - if !aligned { - return Err(anyhow::anyhow!( - "GWAS summary statistics files are not aligned!" - )); - } - let tag_info = Arc::new(tag_info); - - let (result_sender, result_receiver) = crossbeam_channel::unbounded::(); - let n_paths = gwas_paths.len() as u64; - let pb = make_progressbar(n_paths * (n_paths - 1) / 2); - - type Stats<'a> = &'a [Arc]; - let compute = |left: Stats, right: Stats, same: bool| { - compute_rg_chunk( - left, - right, - same, - &result_sender, - &tag_info, - &pb, - runtime_setup, - ) - }; - - let writer_process = { - let pb = pb.clone(); - let conn = runtime_setup.db_conn.clone(); - std::thread::spawn(move || rg_result_writer(&result_receiver, &pb, &conn)) - }; - - let chunks = gwas_paths - .chunks(runtime_setup.chunk_size / 2) - .collect::>(); - - for (i, left_chunk) in chunks.iter().enumerate() { - let left_chunk = left_chunk.to_vec(); - let left_sumstats = load_phenotypes_chunk(&left_chunk, &tag_info, runtime_setup)?; - - compute(&left_sumstats, &left_sumstats, true)?; - - for (j, right_chunk) in chunks.iter().enumerate() { - if i >= j { - continue; - } - let right_chunk = right_chunk.to_vec(); - let right_sumstats = load_phenotypes_chunk(&right_chunk, &tag_info, runtime_setup)?; - - compute(&left_sumstats, &right_sumstats, false)?; - } - } - - drop(result_sender); - writer_process.join().unwrap()?; - - Ok(()) -} diff --git a/src/io/common.rs b/src/io/common.rs new file mode 100644 index 0000000..e19eaae --- /dev/null +++ b/src/io/common.rs @@ -0,0 +1,30 @@ +use std::fs::File; +use std::io::{BufRead, BufReader}; +use std::path::Path; + +use anyhow::{bail, Result}; +use serde::Serializer; + +pub fn get_delimiter

(path: P) -> Result +where + P: AsRef, +{ + let file = File::open(path)?; + let reader = BufReader::new(file); + let first_line = reader.lines().next().unwrap()?; + + if !first_line.starts_with("Predictor") { + bail!("First line does not start with 'Predictor'"); + } + + let delimiter = first_line.as_bytes()[9]; + + Ok(delimiter) +} + +pub fn round_serialize(x: &f64, s: S) -> Result +where + S: Serializer, +{ + s.serialize_str(&format!("{:.6}", x)) +} diff --git a/src/io/gwas.rs b/src/io/gwas.rs index 7fb62b9..76e0215 100644 --- a/src/io/gwas.rs +++ b/src/io/gwas.rs @@ -1,118 +1,91 @@ -use std::path::{Path, PathBuf}; +use std::fs::File; +use std::path::Path; use anyhow::Result; -use crossbeam_channel::{Receiver, Sender}; use csv::ReaderBuilder; - +use itertools::izip; use serde::Deserialize; +use crate::io::common::get_delimiter; + #[derive(Clone, Debug, Deserialize)] -pub struct GwasResultLine { +pub struct GwasLine { #[serde(rename = "Predictor")] pub predictor: String, - pub n: f64, + pub n: u32, #[serde(rename = "Z")] pub z: f64, } -pub struct RawGwasSumstats { +#[derive(Clone, Debug)] +pub struct GwasSumstats { pub phenotype: String, - pub results: Vec, -} + pub results: Vec, -pub struct AlignedGwasSumstats { - pub phenotype: String, + pub predictors: Vec, + pub z_scores: Vec, pub chisq: Vec, - pub sample_sizes: Vec, + pub sample_size: Vec, pub rhos: Vec, } -/// Read GWAS summary statistics from an LDAK-formatted file. -pub fn read_sumstats(path: &Path) -> Result { - let mut reader = ReaderBuilder::new() - .has_headers(true) - .delimiter(b'\t') - .from_path(path)?; - - let mut results = Vec::new(); - for result in reader.deserialize() { - let record: GwasResultLine = result?; - results.push(record); +impl GwasSumstats { + pub fn new(phenotype: String, results: Vec) -> Self { + let predictors = results + .iter() + .map(|x| x.predictor.clone()) + .collect::>(); + let z_scores = results.iter().map(|x| x.z).collect::>(); + let chisq = results.iter().map(|x| x.z * x.z).collect::>(); + let sample_size = results.iter().map(|x| x.n as f64).collect::>(); + + let mut rhos = Vec::with_capacity(results.len()); + for (&z, &c, &n) in izip!(&z_scores, &chisq, &sample_size) { + rhos.push(z.signum() * (c / (c + n)).sqrt()); + } + + GwasSumstats { + phenotype, + results, + predictors, + chisq, + sample_size, + z_scores, + rhos, + } } - let phenotype = path.to_str().unwrap().to_string(); - - Ok(RawGwasSumstats { phenotype, results }) -} - -fn align_sumstats( - predictor_order: &[String], - raw_stats: &[GwasResultLine], -) -> Result> { - let aligned_stats = raw_stats - .iter() - .filter(|s| predictor_order.iter().any(|p| p == &s.predictor)) - .cloned() - .collect::>(); - - Ok(aligned_stats) -} - -pub fn process_sumstats( - predictor_order: &[String], - raw_stats: &RawGwasSumstats, -) -> Result { - let is_aligned = predictor_order - .iter() - .zip(raw_stats.results.iter()) - .all(|(p, s)| p == &s.predictor); - - let aligned_vec: Vec; - let aligned_stats: &[GwasResultLine]; - - if is_aligned { - aligned_stats = &raw_stats.results; - } else { - println!("WARNING: Aligning {}", raw_stats.phenotype); - aligned_vec = align_sumstats(predictor_order, &raw_stats.results)?; - aligned_stats = &aligned_vec; - } - - let mut chisq = Vec::new(); - let mut sample_sizes = Vec::new(); - let mut rhos = Vec::new(); - - for row in aligned_stats.iter() { - let chisq_i = row.z.powi(2); - chisq.push(chisq_i); - sample_sizes.push(row.n); - rhos.push(row.z.signum() * (chisq_i / (chisq_i + row.n)).sqrt()); - } - - Ok(AlignedGwasSumstats { - phenotype: raw_stats.phenotype.clone(), - chisq, - sample_sizes, - rhos, - }) -} - -pub fn sumstat_reader(gwas_paths: &[PathBuf], raw_channel: &Sender) -> Result<()> { - for path in gwas_paths { - let results = read_sumstats(path)?; - raw_channel.send(results)?; - } - Ok(()) -} - -pub fn sumstat_processor( - predictor_order: &[String], - raw_channel: &Receiver, - processed_channel: &Sender, -) -> Result<()> { - for raw_stats in raw_channel { - let aligned_stats = process_sumstats(predictor_order, &raw_stats)?; - processed_channel.send(aligned_stats)?; + /// Read GWAS summary statistics from an LDAK-formatted file. + pub fn from_file

(path: P) -> Result + where + P: AsRef, + { + let delimiter = get_delimiter(&path)?; + + let file = File::open(&path)?; + let mut reader = ReaderBuilder::new() + .has_headers(true) + .delimiter(delimiter) + .from_reader(file); + + let mut results = reader + .deserialize() + .collect::, csv::Error>>()?; + + results.iter_mut().for_each(|x| { + if x.z == 0.0 { + x.z = 1e-6; + } + }); + + let phenotype = path + .as_ref() + .file_name() + .unwrap() + .to_str() + .unwrap() + .to_string(); + + Ok(GwasSumstats::new(phenotype, results)) } - Ok(()) } diff --git a/src/io/mod.rs b/src/io/mod.rs index dab7ca0..3f3faef 100644 --- a/src/io/mod.rs +++ b/src/io/mod.rs @@ -1,2 +1,3 @@ +pub mod common; pub mod gwas; pub mod tagging; diff --git a/src/io/tagging.rs b/src/io/tagging.rs index d6ca494..8efc94d 100644 --- a/src/io/tagging.rs +++ b/src/io/tagging.rs @@ -1,17 +1,109 @@ -use anyhow::{Context, Result}; -use csv::ReaderBuilder; -use ndarray::prelude::*; -use polars::prelude::*; use std::fs::File; -use std::io::prelude::*; -use std::io::BufReader; - -#[derive(Debug, Clone)] -pub struct CategoryInfo { - pub n_variants: usize, - pub n_categories: usize, - pub names: Vec, +use std::io::{BufRead, BufReader}; +use std::path::Path; + +use anyhow::Result; + +#[derive(Clone, Debug)] +pub struct TagLine { + pub predictor: String, + pub tagging: f64, + pub annotations: Vec, +} + +impl TagLine { + pub fn new(predictor: String, tagging: f64, annotations: Vec) -> Self { + Self { + predictor, + tagging, + annotations, + } + } + + pub fn from_str(line: &str) -> Result { + let parts = line.split_whitespace().collect::>(); + let predictor = parts[0].to_string(); + let tagging = parts[4].parse()?; + let annotations = parts[9..].iter().map(|x| x.parse().unwrap()).collect(); + Ok(Self::new(predictor, tagging, annotations)) + } +} + +#[derive(Clone, Debug)] +pub struct TagInfo { + pub taglines: Vec, + pub annotation_names: Vec, pub ssums: Vec>, + + pub predictors: Vec, + pub tagging: Vec, + pub annotations: Vec>, +} + +impl TagInfo { + pub fn new( + taglines: Vec, + annotation_names: Vec, + ssums: Vec>, + ) -> Self { + let predictors = taglines.iter().map(|x| x.predictor.clone()).collect(); + let tagging = taglines.iter().map(|x| x.tagging).collect(); + + let n_annotations = taglines[0].annotations.len(); + let mut annotations = vec![vec![0.0; taglines.len()]; n_annotations]; + + for (i, tagline) in taglines.iter().enumerate() { + for (j, annotation) in tagline.annotations.iter().enumerate() { + annotations[j][i] = *annotation; + } + } + + Self { + taglines, + annotation_names, + ssums, + predictors, + tagging, + annotations, + } + } + + pub fn from_file

(file: P) -> Result + where + P: AsRef, + { + let file = File::open(file).unwrap(); + let reader = BufReader::new(file); + + let mut header_line = String::new(); + let mut tag_lines = Vec::new(); + let mut contrib_lines = Vec::new(); + let mut final_line = String::new(); + + let mut reached_end = false; + + for (i, row) in reader.lines().enumerate() { + let line = row?; + + if i == 0 { + header_line = line; + } else if line.starts_with("The") { + reached_end = true; + if line.starts_with("There") { + final_line = line; + } else { + contrib_lines.push(line); + } + } else if !reached_end { + tag_lines.push(TagLine::from_str(&line)?); + } + } + + let category_names = header_line_to_category_names(&header_line); + let ssums = final_lines_to_ssums(&contrib_lines, &final_line); + + Ok(Self::new(tag_lines, category_names, ssums)) + } } fn header_line_to_category_names(header_line: &str) -> Vec { @@ -65,148 +157,3 @@ fn final_lines_to_ssums(contrib_lines: &[String], final_line: &str) -> Vec Result { - let file = File::open(filename)?; - let buf_reader = BufReader::new(file); - - let mut header_line = String::new(); - let mut n_variants = 0; - let mut contrib_lines = Vec::new(); - let mut final_line = String::new(); - - for (i, row) in buf_reader.lines().enumerate() { - let line = row?; - - if i == 0 { - header_line = line; - } else if line.starts_with("The") { - if n_variants == 0 { - // Number of rows after header before tag info lines - n_variants = i - 1; - } - - if line.starts_with("There") { - final_line = line; - } else { - contrib_lines.push(line); - } - } - } - - let category_names = header_line_to_category_names(&header_line); - let ssums = final_lines_to_ssums(&contrib_lines, &final_line); - - Ok(CategoryInfo { - n_variants, - n_categories: category_names.len(), - names: category_names, - ssums, - }) -} - -#[derive(Clone)] -pub struct TagInfo { - pub df: DataFrame, - pub category_info: CategoryInfo, - - pub predictor_order: Vec, - pub tag_vec: Vec, - pub cat_vec: Vec>, -} - -impl TagInfo { - pub fn from_dataframe(df: DataFrame, category_info: CategoryInfo) -> Result { - let predictor_order = df - .column("Predictor")? - .utf8()? - .into_iter() - .map(|x| x.expect("Could not convert Predictor column").to_string()) - .collect::>(); - - let tag_vec = df - .column("Tagging")? - .f64()? - .into_iter() - .collect::>>() - .context("Tagging column contains null values!")?; - - let cat_vec = df - .select(category_info.names.iter())? - .to_ndarray::(IndexOrder::Fortran)? - .axis_iter(Axis(1)) - .map(|x| x.to_vec()) - .collect::>>(); - - Ok(Self { - df, - category_info, - predictor_order, - tag_vec, - cat_vec, - }) - } - - pub fn update_from_dataframe(&mut self, df: DataFrame) -> Result<()> { - let predictor_order = df - .column("Predictor")? - .utf8()? - .into_iter() - .map(|x| x.expect("Could not convert Predictor column").to_string()) - .collect::>(); - - let tag_vec = df - .column("Tagging")? - .f64()? - .into_iter() - .collect::>>() - .context("Tagging column contains null values!")?; - - let cat_vec = df - .select(self.category_info.names.iter())? - .to_ndarray::(IndexOrder::Fortran)? - .axis_iter(Axis(1)) - .map(|x| x.to_vec()) - .collect::>>(); - - self.df = df; - self.predictor_order = predictor_order; - self.tag_vec = tag_vec; - self.cat_vec = cat_vec; - - Ok(()) - } -} - -pub fn read_tagfile(filename: &str) -> Result { - let category_info = read_category_info(filename)?; - - let mut csv_reader = ReaderBuilder::new() - .has_headers(true) - .delimiter(b' ') - .from_path(filename)?; - - let header = csv_reader.headers()?.clone(); - let mut schema = Schema::new(); - - header.iter().for_each(|x| { - schema.with_column( - x.into(), - match x { - "Predictor" => DataType::Utf8, - _ => DataType::Float64, - }, - ); - }); - - let df = CsvReader::from_path(filename)? - .has_header(true) - .with_separator(b' ') - .with_n_rows(Some(category_info.n_variants)) - .with_ignore_errors(true) - .with_dtypes(Some(Arc::new(schema))) - .finish() - .with_context(|| format!("Failed to read tagfile {}", filename))?; - - TagInfo::from_dataframe(df, category_info) -} diff --git a/src/ldak/sumfuns.c b/src/ldak/sumfuns.c index 85b02a4..00cef07 100644 --- a/src/ldak/sumfuns.c +++ b/src/ldak/sumfuns.c @@ -37,6 +37,60 @@ int solve_sums(double *stats, double *likes, double *cohers, double *influs, // sflag=3 - just get expectations and likelihood, sflag=4 - LDSC, sflag=5 - // divide+updating { + // Print the first few of each input variable + // printf("num_parts: %d\n", num_parts); + // printf("gcon: %d\n", gcon); + // printf("cept: %d\n", cept); + // printf("num_blocks: %d\n", num_blocks); + // printf("length: %d\n", length); + // printf("ncv: %d\n", ncv); + // + // printf("cvindex: "); + // for (int i = 0; i < ncv; i++) { + // printf("%d ", cvindex[i]); + // } + // printf("\n"); + // + // printf("cvexps: "); + // for (int i = 0; i < ncv; i++) { + // printf("%f ", cvexps[i]); + // } + // printf("\n"); + // + // printf("stags: "); + // for (int i = 0; i < 3; i++) { + // printf("%f ", stags[i]); + // } + // printf("\n"); + // + // printf("svars: "); + // for (int i = 0; i < num_parts; i++) { + // for (int k = 0; k < 3; k++) { + // printf("%f ", svars[i][k]); + // } + // } + // printf("\n"); + // + // printf("ssums: "); + // for (int i = 0; i < num_parts; i++) { + // for (int k = 0; k < (num_parts + 2); k++) { + // printf("%f ", ssums[i][k]); + // } + // } + // printf("\n"); + // + // printf("snss: "); + // for (int i = 0; i < 3; i++) { + // printf("%f ", snss[i]); + // } + // printf("\n"); + // + // printf("schis: "); + // for (int i = 0; i < 3; i++) { + // printf("%f ", schis[i]); + // } + // printf("\n"); + int return_code = 0; int j, j2, p, q, q2, q3, count, count2, start, end, mark, one = 1; @@ -279,6 +333,25 @@ int solve_sums(double *stats, double *likes, double *cohers, double *influs, sumhers += thetas[q] / gc * ssums[q][q] / scale; } + // if (count == 0) { + // printf("Start\t"); + // } else { + // printf("%d\t", count); + // } + // printf("%.4f\t", sumhers); + // if (gcon == 1) { + // printf("%.4f\t", gc); + // } + // if (cept == 1) { + // printf("%.4f\t", 1 + thetas[num_parts + gcon] / gc); + // } + // printf("%.2f\t", like); + // if (count == 0) { + // printf("n/a\t\t%.6f\n", tol); + // } else { + // printf("%.6f\t%.6f\n", diff, tol); + // } + if (sflag == 3) { break; } // only wanted expectations and likelihood diff --git a/src/main.rs b/src/main.rs index 7745d50..109023c 100644 --- a/src/main.rs +++ b/src/main.rs @@ -2,14 +2,15 @@ use clap::{Args, Parser, Subcommand}; use glob::glob; use std::path::PathBuf; +mod align; mod db; mod ffi; mod hsq; mod io; +mod rg; mod util; use crate::db::DbConnection; -use crate::hsq::{compute_h2, compute_rg}; use crate::util::{format_plink_sumstats, RuntimeSetup}; #[derive(Parser, Debug)] @@ -69,7 +70,7 @@ enum Command { #[arg(long)] rg_tagfile: PathBuf, }, - /// Compute just heritabilities + // Compute just heritabilities H2 { #[command(flatten)] shared_args: SharedArgs, @@ -78,7 +79,6 @@ enum Command { #[arg(short, long)] tagfile: PathBuf, }, - /// Compute just genetic correlations Rg { #[command(flatten)] @@ -91,6 +91,11 @@ enum Command { } fn validate_shared_args(args: &mut SharedArgs) -> RuntimeSetup { + rayon::ThreadPoolBuilder::new() + .num_threads(args.n_threads) + .build_global() + .unwrap(); + if args.gwas_results.is_empty() { panic!("No GWAS results files specified"); } @@ -137,13 +142,13 @@ fn main() { rg_tagfile, } => { let rt = validate_shared_args(&mut shared_args); - let result = compute_h2(&h2_tagfile, &shared_args.gwas_results, &rt); + let result = hsq::compute_h2(h2_tagfile, &shared_args.gwas_results, &rt); match result { Ok(_) => println!("Success on heritability!"), Err(e) => println!("Error: {}", e), } - let rg_result = compute_rg(&rg_tagfile, &shared_args.gwas_results, &rt); + let rg_result = rg::compute_rg(rg_tagfile, &shared_args.gwas_results, &rt); match rg_result { Ok(_) => println!("Success on genetic correlation!"), Err(e) => println!("Error: {}", e), @@ -154,7 +159,8 @@ fn main() { tagfile, } => { let rt = validate_shared_args(&mut shared_args); - let result = compute_h2(&tagfile, &shared_args.gwas_results, &rt); + let result = hsq::compute_h2(tagfile, &shared_args.gwas_results, &rt); + // let result = compute_h2(&tagfile, &shared_args.gwas_results, &rt); match result { Ok(_) => println!("Success on heritability!"), Err(e) => println!("Error: {}", e), @@ -165,7 +171,7 @@ fn main() { tagfile, } => { let rt = validate_shared_args(&mut shared_args); - let result = compute_rg(&tagfile, &shared_args.gwas_results, &rt); + let result = rg::compute_rg(tagfile, &shared_args.gwas_results, &rt); match result { Ok(_) => println!("Success on genetic correlation!"), Err(e) => println!("Error: {}", e), diff --git a/src/rg.rs b/src/rg.rs new file mode 100644 index 0000000..b2ab775 --- /dev/null +++ b/src/rg.rs @@ -0,0 +1,195 @@ +use std::path::{Path, PathBuf}; + +use anyhow::Result; +use itertools::Itertools; +use rayon::prelude::*; +use serde::Serialize; + +use crate::align::{align_gwas_gwas, check_aligned}; +use crate::ffi::{solve_cors_wrapper, SolveCorsResult}; +use crate::io::common::round_serialize; +use crate::io::gwas::GwasSumstats; +use crate::io::tagging::TagInfo; +use crate::util::{make_progressbar, RuntimeSetup}; + +pub fn compute_rg

( + tag_path: P, + gwas_paths: &[PathBuf], + runtime_setup: &RuntimeSetup, +) -> Result<()> +where + P: AsRef, +{ + let n_combos = gwas_paths.len() * (gwas_paths.len() - 1) / 2; + let pb = make_progressbar(n_combos as u64); + + let tag_info = TagInfo::from_file(tag_path)?; + + let chunks: Vec> = gwas_paths + .iter() + .chunks(runtime_setup.chunk_size / 2) + .into_iter() + .map(|x| x.cloned().collect::>()) + .collect::>(); + + for (i, left_chunk) in chunks.iter().enumerate() { + let left_stats = load_gwas_chunk(left_chunk)?; + let left_results = left_stats + .iter() + .combinations(2) + .collect::>() + .par_iter() + .map(|x| wrap_rg(&mut tag_info.clone(), &mut x[0].clone(), &mut x[1].clone())) + .collect::>>()?; + + runtime_setup + .db_conn + .lock() + .unwrap() + .write_rg(&left_results.into_iter().flatten().collect::>())?; + + for right_chunk in chunks.iter().skip(i) { + let right_stats = load_gwas_chunk(right_chunk)?; + + let combos = left_stats + .iter() + .cartesian_product(right_stats.iter()) + .filter(|(x, y)| { + !runtime_setup + .computed + .finished_rg + .contains(&(x.phenotype.clone(), y.phenotype.clone())) + }) + .collect::>(); + + let results = combos + .par_iter() + .map(|(x, y)| { + let result = + wrap_rg(&mut tag_info.clone(), &mut (*x).clone(), &mut (*y).clone()); + pb.lock().unwrap().inc(1); + result + }) + .collect::>>()?; + + runtime_setup + .db_conn + .lock() + .unwrap() + .write_rg(&results.into_iter().flatten().collect::>())?; + } + } + + Ok(()) +} + +fn load_gwas_chunk(files: &[PathBuf]) -> Result> { + files.iter().map(GwasSumstats::from_file).collect() +} + +fn wrap_rg( + tag_info: &mut TagInfo, + gwas1: &mut GwasSumstats, + gwas2: &mut GwasSumstats, +) -> Result> { + if !check_aligned(gwas1, tag_info) || !check_aligned(gwas2, tag_info) { + (*gwas1, *gwas2, *tag_info) = align_gwas_gwas(gwas1, gwas2, tag_info); + } + + let result = solve_cors_wrapper( + &tag_info.tagging, + gwas1, + gwas2, + &tag_info.annotations, + &tag_info.ssums, + None, + )?; + + Ok(format_genetic_correlation( + gwas1.phenotype.clone(), + gwas2.phenotype.clone(), + &result, + )) +} + +#[derive(Debug, Serialize)] +pub struct RgResult { + pub phenotype1: String, + pub phenotype2: String, + pub component: String, + + #[serde(serialize_with = "round_serialize")] + pub estimate: f64, + + #[serde(serialize_with = "round_serialize")] + pub se: f64, +} + +fn format_genetic_correlation( + phenotype1: String, + phenotype2: String, + result: &SolveCorsResult, +) -> Vec { + let num_parts = result.num_parts as usize; + let total = 2 * (result.gcon + result.cept) as usize + 3 * num_parts + 1; + let total2 = num_parts + (result.gcon + result.cept) as usize; + let se_idx = 2 * total + 4 + num_parts; + + let mut partitions = vec![ + RgResult { + phenotype1: phenotype1.clone(), + phenotype2: phenotype2.clone(), + component: "Her1_All".to_string(), + estimate: result.stats[total], + se: result.stats[se_idx], + }, + RgResult { + phenotype1: phenotype1.clone(), + phenotype2: phenotype2.clone(), + component: "Her2_All".to_string(), + estimate: result.stats[total + 1], + se: result.stats[se_idx + 1], + }, + RgResult { + phenotype1: phenotype1.clone(), + phenotype2: phenotype2.clone(), + component: "Coher_All".to_string(), + estimate: result.stats[total + 2], + se: result.stats[se_idx + 2], + }, + RgResult { + phenotype1: phenotype1.clone(), + phenotype2: phenotype2.clone(), + component: "Cor_All".to_string(), + estimate: result.stats[total + 3], + se: result.stats[se_idx + 3], + }, + ]; + + if result.gcon == 1 { + partitions.push(RgResult { + phenotype1: phenotype1.clone(), + phenotype2: phenotype2.clone(), + component: "Scaling1".to_string(), + estimate: result.stats[num_parts], + se: result.stats[2 * num_parts + 4 + total], + }); + partitions.push(RgResult { + phenotype1: phenotype1.clone(), + phenotype2: phenotype2.clone(), + component: "Scaling2".to_string(), + estimate: result.stats[total2 + num_parts], + se: result.stats[2 * num_parts + 4 + total + total2], + }); + } + + partitions.push(RgResult { + phenotype1: phenotype1.clone(), + phenotype2: phenotype2.clone(), + component: "Overlap".to_string(), + estimate: result.stats[2 * total2 + num_parts], + se: result.stats[2 * num_parts + 4 + total + 2 * total2], + }); + + partitions +} diff --git a/src/util.rs b/src/util.rs index 9377fd9..bb5a451 100644 --- a/src/util.rs +++ b/src/util.rs @@ -2,12 +2,11 @@ use indicatif::ProgressBar; use std::path::{Path, PathBuf}; use std::sync::{Arc, Mutex}; -use crate::db::{DbConnection, Progress}; -use crate::io::tagging::TagInfo; - use anyhow::Result; -use csv::ReaderBuilder; -use polars::prelude::*; +use csv::{ReaderBuilder, WriterBuilder}; +use serde::{Deserialize, Serialize}; + +use crate::db::{DbConnection, Progress}; pub struct RuntimeSetup { pub n_threads: usize, @@ -46,128 +45,39 @@ pub fn make_progressbar(n_total: u64) -> Arc> { Arc::new(Mutex::new(pb)) } +#[derive(Clone, Debug, Deserialize, Serialize)] +struct PlinkSumstats { + #[serde(rename(serialize = "Predictor", deserialize = "ID"))] + predictor: String, + #[serde(rename = "A1")] + a1: String, + #[serde(rename(serialize = "A2", deserialize = "OMITTED"))] + a2: String, + #[serde(rename(serialize = "n", deserialize = "OBS_CT"))] + n: f64, + #[serde(rename(serialize = "Z", deserialize = "T_STAT"))] + z: f64, +} + /// Reformat Plink summary statistics files for use with LDAK pub fn format_plink_sumstats

(gwas_path: P, output_path: P) -> Result<()> where P: Into + AsRef, { - let mut df = CsvReader::from_path(gwas_path)? - .has_header(true) - .with_ignore_errors(true) - .with_comment_char(Some(b'?')) - .with_separator(b'\t') - .finish()?; - - df = df - .lazy() - .select(&[ - col("ID").alias("Predictor"), - col("A1"), - col("OMITTED").alias("A2"), - col("OBS_CT").alias("n"), - col("T_STAT").alias("Z"), - ]) - .collect()?; - - let mut file = std::fs::File::create(output_path)?; - - CsvWriter::new(&mut file) - .include_header(true) - .with_separator(b'\t') - .finish(&mut df) - .expect("Error writing output file"); - - Ok(()) -} - -/// Read Predictors from LDAK-format GWAS summary statistics files -/// Predictors are the SNP IDs, either rsIDs or chr:pos -fn read_predictors(path: &Path) -> Result> { let mut reader = ReaderBuilder::new() - .has_headers(true) .delimiter(b'\t') - .from_path(path)?; - - let predictor_idx = reader - .headers()? - .iter() - .position(|x| x == "Predictor") - .ok_or_else(|| anyhow::anyhow!("Could not find Predictor column"))?; - - let mut predictors = Vec::new(); - for result in reader.records() { - let record = result?; - predictors.push(record.get(predictor_idx).unwrap().to_string()); - } - Ok(predictors) -} - -fn compare_predictors(path: &Path, comparison: &[String]) -> Result { - let mut reader = ReaderBuilder::new() .has_headers(true) - .delimiter(b'\t') - .from_path(path)?; + .buffer_capacity(8 * (1 << 20)) + .from_path(&gwas_path)?; - let predictor_idx = reader - .headers()? - .iter() - .position(|x| x == "Predictor") - .ok_or_else(|| anyhow::anyhow!("Could not find Predictor column"))?; + let mut writer = WriterBuilder::new() + .delimiter(b' ') + .buffer_capacity(8 * (1 << 20)) + .from_path(&output_path)?; - for (i, result) in reader.records().enumerate() { - let record = result?; - let predictor = record.get(predictor_idx).unwrap(); - if comparison[i] != predictor { - return Ok(false); - } + for record in reader.deserialize::() { + writer.serialize(record?)?; } - Ok(true) -} - -/// Check if predictors are aligned across GWAS summary statistics files -/// If so, return the shared predictors. Aligned predictors enable much -/// faster computation. -pub fn check_predictors_aligned( - gwas_paths: &[PathBuf], - skip_check: bool, -) -> Result> { - let first_series = read_predictors(&gwas_paths[0])?; - let pb = make_progressbar(gwas_paths.len() as u64); - - let mut aligned = true; - if !skip_check { - for path in gwas_paths.iter().skip(1) { - let result = compare_predictors(path, &first_series)?; - aligned = aligned && result; - pb.lock().unwrap().inc(1); - } - } - - if aligned { - let series = Series::new("Predictor", &first_series); - Ok(Some(series.into_frame())) - } else { - Ok(None) - } -} - -/// Align predictors from the tag file with the predictors from the GWAS summary statistics files -pub fn align_if_possible(tag_info: &mut TagInfo, alignment: Option) -> Result { - match alignment { - Some(shared_predictors) => { - let new_df = tag_info - .df - .join( - &shared_predictors, - ["Predictor"], - ["Predictor"], - JoinArgs::new(JoinType::Inner), - ) - .unwrap(); - tag_info.update_from_dataframe(new_df)?; - Ok(true) - } - None => Ok(false), - } + Ok(()) } diff --git a/tests/README.md b/tests/README.md index 8455b2d..39842ea 100644 --- a/tests/README.md +++ b/tests/README.md @@ -34,7 +34,7 @@ xsv join -d ' ' Predictor ldak.thin.genotyped.gbr.tagging Predictor neur.txt.old # Height xsv join -d ' ' Predictor ldak.thin.genotyped.gbr.tagging Predictor height.txt.old | - xsv select 'Predictor,A1,A2,Direction,Stat,n' | + xsv select 'Predictor,A1,A2,Z,n' | xsv fmt -t ' ' -o height.txt ``` diff --git a/tests/data/height.tsv b/tests/data/height.tsv new file mode 100644 index 0000000..ab140b1 --- /dev/null +++ b/tests/data/height.tsv @@ -0,0 +1,143246 @@ +Predictor A1 A2 Z n +1:768448 G A -0.602273 88015 +1:779322 A G 0.047619 136071 +1:1003629 C T -2.13158 240455 +1:1005806 C T -0.0612245 190854 +1:1018704 A G 1.45455 244492 +1:1030565 C T 0.173913 199778 +1:1031540 A G 1.5 188012 +1:1062638 C A -1.74359 182659 +1:1099342 A C 0.186441 246624 +1:1110019 A G 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372903 +22:50709226 G A 1.423 372903 +22:50709415 G T -0.708 372903 +22:50715888 G A -0.254 372903 +22:50716167 G A -1.869 372903 +22:50716480 C T 2.163 370708 +22:50717129 T G 1.78 372903 +22:50717787 C A 1.654 372903 +22:50721492 C T 0.143 372903 +22:50721756 G A 0.961 372903 +22:50722134 T C 1.856 372903 +22:50722167 T C -1.691 372903 +22:50722408 T C -0.763 372903 +22:50726627 G A 1.324 372903 +22:50727782 G A -0.465 372903 +22:50728062 T C -0.532 372903 +22:50731310 A G 0.072 372903 +22:50734890 C T -0.216 372903 +22:50735872 C T 1.014 372903 +22:50739049 G A 0.186 372903 +22:50742935 A G -1.588 372903 +22:50752150 C T -1.176 372903 +22:50754466 C T -1.229 372903 +22:50754512 C T 0.516 372903 +22:50757470 T C 0.787 372903 +22:50758873 C T 1.068 372903 +22:50764408 A C -2.059 372903 +22:50786976 G A 0.317 372903 +22:50803458 T C 0.41 372903 +22:50805537 G A -0.204 372903 +22:50809482 G A -1.269 372903 +22:50814075 C T -0.67 372903 +22:50815903 G A 0.704 372903 +22:50820671 A G 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T C 0.437 372903 +22:50936324 T C 0.595 372903 +22:50937043 A C -0.279 372903 +22:50939714 G A 1.535 372903 +22:50943423 G A 3.448 372903 +22:50943506 C T 0.882 372903 +22:50946965 T C -0.13 371949 +22:50947196 T C 1.004 372903 +22:50950564 A C 0.712 372903 +22:50951347 A G 2.364 372903 +22:50952730 G A -1.245 372903 +22:50952989 G A 0.664 372903 +22:50955538 A G -0.758 390278 +22:50957733 C T -0.398 372903 +22:50959608 C T 0.284 390278 +22:50960682 C T -2.168 372903 +22:50961169 A G 1.144 372903 +22:50962259 G A -0.415 372903 +22:50966914 T C -0.506 372903 +22:50970068 C T -0.194 372903 +22:50971266 T C -0.396 372903 +22:50971752 A C 1.573 372903 +22:50978024 C A -0.697 390278 +22:50978262 G A -2.906 372903 +22:50981043 C T 2.554 372903 +22:50981340 C T -1.022 372903 +22:50983936 A G 1.041 372903 +22:50986647 G A 2.013 371967 +22:50987287 A G 1.489 367987 +22:50987843 C T -0.282 372903 +22:50988062 G T 1.721 390278 +22:50988105 G A -0.457 372903 +22:50988193 A G -1.463 390278 +22:50989197 C T 1.234 372903 +22:50989326 A G -1.398 390278 +22:50989678 A G 0.519 372903 +22:50996974 C A -0.495 372903 +22:50997261 C T -0.603 372903 +22:50999538 A G 0.192 372903 +22:50999681 A G 0.008 372903 +22:51004053 T C -0.672 390278 +22:51004876 A G 0.472 372903 +22:51008925 G A -1.633 390278 +22:51009953 C T 0.652 390278 +22:51015572 C T 1.613 372903 +22:51015838 T C 1.847 390278 +22:51017353 T C 2.259 390278 +22:51024624 T C -1.107 390278 +22:51033119 T C 1.693 372903 +22:51035829 G A -1.573 372903 +22:51035885 C T 0.37 372903 +22:51041663 C A -0.603 372903 +22:51043278 G A -1.605 367458 +22:51045190 C T -1.429 372903 +22:51048400 A G -2.319 390278 +22:51048721 G A -2.152 372903 +22:51061827 C T 0.201 372903 +22:51063477 T C -1.574 372903 +22:51064416 T C -1.614 372903 +22:51065229 G A -0.307 372903 +22:51065361 C A -1.439 372903 +22:51065600 G A -0.23 390278 +22:51068560 G A 0.344 372903 +22:51079446 A G -1.078 372903 +22:51090768 C T -0.273 368093 +22:51094492 C T -3.32 372903 +22:51094926 C T 1.821 372903 +22:51103091 T C 1.829 372903 +22:51104680 G A -2.378 390278 +22:51109717 G A -1.149 372903 +22:51114518 C T -3.206 372903 +22:51117580 T C 3.464 390278 +22:51121521 C T -0.462 390278 +22:51122593 C A 0.584 372903 +22:51123287 A G -0.175 372903 +22:51123467 T C 2.164 372903 +22:51125913 A G 0.275 372903 +22:51126986 C T -2.245 372903 +22:51134387 G A -0.307 372903 +22:51134650 G A -0.625 371233 +22:51136408 C T -1.286 370654 +22:51138753 A G 1.475 372903 +22:51139380 T C 1.691 369107 +22:51140316 C T -0.565 390278 +22:51142381 G A 0.389 372903 +22:51142979 G T -0.697 372903 +22:51144731 T C 0.014 372903 +22:51145781 C T -2.387 372903 +22:51146139 A G 0.238 390278 +22:51146439 A G 2.239 390278 +22:51147015 A G 0.812 372903 +22:51148424 G A -1 372903 +22:51148993 C T 0.294 372903 +22:51150167 T C -0.042 372903 +22:51150473 G A -0.793 372903 +22:51150771 A G 0.508 372903 +22:51151464 A G -2.262 372903 +22:51151684 G A 2.119 372903 +22:51151724 C T 0.056 372903 +22:51152554 A G 1.009 372903 +22:51154982 C T 1.107 372903 +22:51156666 C T -0.755 372903 +22:51157353 C T -0.218 372903 +22:51157483 C T -1.35 369714 +22:51161019 C T 0.223 372903 +22:51161093 C T 0.494 372903 +22:51162059 G A 0.494 372903 +22:51163138 C T -1.213 372903 +22:51163910 C T 2.007 372903 +22:51165664 G A 0.468 372903 +22:51171497 G A -0.881 372903 +22:51173542 T C -0.071 372903 +22:51174939 C T 0.174 372903 +22:51175626 A G -1.85 372903 +22:51177257 C T -1.642 372903 +22:51185848 G A 0.628 372903 +22:51193629 A G 0.11 372903 +22:51217954 G A -0.677 372903 diff --git a/tests/full_test.rs b/tests/full_test.rs index 71c869f..4a910b9 100644 --- a/tests/full_test.rs +++ b/tests/full_test.rs @@ -5,8 +5,12 @@ use std::process::Command; use assert_cmd::prelude::*; #[test] -fn cli_h2() { +fn cli_h2_neur() { compute_h2("neur"); +} + +#[test] +fn cli_h2_height() { compute_h2("height"); } @@ -111,76 +115,76 @@ fn load_ldak_h2_results(phenotype: &str) -> H2Result { results } -#[test] -fn compute_rg() { - let mut d = PathBuf::from(env!("CARGO_MANIFEST_DIR")); - d.push("tests/data/"); - - let output_dir = tempfile::tempdir().unwrap(); - let output = output_dir.path().join("output.db"); - - let mut cmd = Command::cargo_bin("sumher_rs").unwrap(); - let assert = cmd - .arg("rg") - .arg("-g") - .arg(d.join("neur.txt").to_str().unwrap()) - .arg(d.join("height.txt").to_str().unwrap()) - .arg("-t") - .arg(d.join("ldak.thin.genotyped.gbr.tagging").to_str().unwrap()) - .arg("-o") - .arg(output.to_str().unwrap()); - - assert.assert().success(); - - let desired_results = load_ldak_rg_results(); - let results = load_sumher_rs_rg_results(&output); - - assert_eq!( - results.phenotype, desired_results.phenotype, - "Phenotypes do not match" - ); - assert_eq!( - results.component, desired_results.component, - "Components do not match" - ); - assert_eq!(results.h2, desired_results.h2, "h2 values do not match"); - assert_eq!( - results.sd, desired_results.sd, - "Standard deviations do not match" - ); -} - -struct RgResult { - phenotype: Vec, - component: Vec, - value: Vec, - sd: Vec, -} - -fn load_ldak_rg_results() -> RgResult { - let path = PathBuf::from(env!("CARGO_MANIFEST_DIR")) - .join("tests/data/") - .join("neur.height.cors"); - - // Open the file at path - let file = std::fs::File::open(path).unwrap(); - let reader = std::io::BufReader::new(file); - - let mut results = RgResult { - phenotype: Vec::new(), - component: Vec::new(), - value: Vec::new(), - sd: Vec::new(), - }; - - reader.lines().skip(1).for_each(|line| { - let line = line.unwrap(); - let fields: Vec<&str> = line.split_whitespace().collect(); - results.phenotype.push(phenotype.to_string() + ".txt"); - results.component.push(fields[0].to_string()); - results.h2.push(fields[1].parse::().unwrap()); - results.sd.push(fields[2].parse::().unwrap()); - }); - - results -} +// #[test] +// fn compute_rg() { +// let mut d = PathBuf::from(env!("CARGO_MANIFEST_DIR")); +// d.push("tests/data/"); +// +// let output_dir = tempfile::tempdir().unwrap(); +// let output = output_dir.path().join("output.db"); +// +// let mut cmd = Command::cargo_bin("sumher_rs").unwrap(); +// let assert = cmd +// .arg("rg") +// .arg("-g") +// .arg(d.join("neur.txt").to_str().unwrap()) +// .arg(d.join("height.txt").to_str().unwrap()) +// .arg("-t") +// .arg(d.join("ldak.thin.genotyped.gbr.tagging").to_str().unwrap()) +// .arg("-o") +// .arg(output.to_str().unwrap()); +// +// assert.assert().success(); +// +// let desired_results = load_ldak_rg_results(); +// let results = load_sumher_rs_rg_results(&output); +// +// assert_eq!( +// results.phenotype, desired_results.phenotype, +// "Phenotypes do not match" +// ); +// assert_eq!( +// results.component, desired_results.component, +// "Components do not match" +// ); +// assert_eq!(results.h2, desired_results.h2, "h2 values do not match"); +// assert_eq!( +// results.sd, desired_results.sd, +// "Standard deviations do not match" +// ); +// } +// +// struct RgResult { +// phenotype: Vec, +// component: Vec, +// value: Vec, +// sd: Vec, +// } +// +// fn load_ldak_rg_results() -> RgResult { +// let path = PathBuf::from(env!("CARGO_MANIFEST_DIR")) +// .join("tests/data/") +// .join("neur.height.cors"); +// +// // Open the file at path +// let file = std::fs::File::open(path).unwrap(); +// let reader = std::io::BufReader::new(file); +// +// let mut results = RgResult { +// phenotype: Vec::new(), +// component: Vec::new(), +// value: Vec::new(), +// sd: Vec::new(), +// }; +// +// reader.lines().skip(1).for_each(|line| { +// let line = line.unwrap(); +// let fields: Vec<&str> = line.split_whitespace().collect(); +// results.phenotype.push(phenotype.to_string() + ".txt"); +// results.component.push(fields[0].to_string()); +// results.h2.push(fields[1].parse::().unwrap()); +// results.sd.push(fields[2].parse::().unwrap()); +// }); +// +// results +// }