From 276f217281d3089a6b09b93f79126e57fbf8050b Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Thu, 28 Dec 2023 14:54:07 +0100 Subject: [PATCH] wip --- src/gnomad_nuclear/cli/import.rs | 62 ++++++++++-- src/gnomad_nuclear/cli/query.rs | 96 +++++++++++++++---- ...t__smoke_query_all@exomes-grch37-2.1.snap} | 0 ...st__smoke_query_all@exomes-grch38-4.0.snap | 11 +++ ...t__smoke_query_all@genomes-grch38-4.0.snap | 12 +++ ...e_query_pos_single@exomes-grch37-2.1.snap} | 0 ...e_query_pos_single@exomes-grch38-4.0.snap} | 0 ..._query_pos_single@genomes-grch38-4.0.snap} | 0 ...ange_find_all_chr1@exomes-grch37-2.1.snap} | 0 ...range_find_all_chr1@exomes-grch38-4.0.snap | 11 +++ ...ange_find_all_chr1@genomes-grch38-4.0.snap | 12 +++ ...y_range_find_first@exomes-grch37-2.1.snap} | 0 ...ry_range_find_first@exomes-grch38-4.0.snap | 5 + ...y_range_find_first@genomes-grch38-4.0.snap | 5 + ...ge_find_none_larger@exomes-grch37-2.1.snap | 5 + ...ge_find_none_larger@exomes-grch38-4.0.snap | 5 + ...e_find_none_larger@genomes-grch38-4.0.snap | 5 + ...e_find_none_smaller@exomes-grch37-2.1.snap | 5 + ...e_find_none_smaller@exomes-grch38-4.0.snap | 11 +++ ..._find_none_smaller@genomes-grch38-4.0.snap | 12 +++ ..._range_find_second@exomes-grch37-2.1.snap} | 0 ...y_range_find_second@exomes-grch38-4.0.snap | 5 + ..._range_find_second@genomes-grch38-4.0.snap | 5 + ...e_query_var_single@exomes-grch37-2.1.snap} | 0 ...ke_query_var_single@exomes-grch38-4.0.snap | 5 + ...e_query_var_single@genomes-grch38-4.0.snap | 5 + 26 files changed, 255 insertions(+), 22 deletions(-) rename src/gnomad_nuclear/cli/snapshots/{annonars__gnomad_nuclear__cli__query__test__smoke_query_exomes_all@exomes-grch37-2.1.snap => annonars__gnomad_nuclear__cli__query__test__smoke_query_all@exomes-grch37-2.1.snap} (100%) create mode 100644 src/gnomad_nuclear/cli/snapshots/annonars__gnomad_nuclear__cli__query__test__smoke_query_all@exomes-grch38-4.0.snap create mode 100644 src/gnomad_nuclear/cli/snapshots/annonars__gnomad_nuclear__cli__query__test__smoke_query_all@genomes-grch38-4.0.snap rename src/gnomad_nuclear/cli/snapshots/{annonars__gnomad_nuclear__cli__query__test__smoke_query_exomes_pos_single@exomes-grch37-2.1.snap => annonars__gnomad_nuclear__cli__query__test__smoke_query_pos_single@exomes-grch37-2.1.snap} (100%) rename src/gnomad_nuclear/cli/snapshots/{annonars__gnomad_nuclear__cli__query__test__smoke_query_exomes_range_find_none_larger@exomes-grch37-2.1.snap => annonars__gnomad_nuclear__cli__query__test__smoke_query_pos_single@exomes-grch38-4.0.snap} (100%) rename src/gnomad_nuclear/cli/snapshots/{annonars__gnomad_nuclear__cli__query__test__smoke_query_exomes_range_find_none_smaller@exomes-grch37-2.1.snap => annonars__gnomad_nuclear__cli__query__test__smoke_query_pos_single@genomes-grch38-4.0.snap} (100%) rename src/gnomad_nuclear/cli/snapshots/{annonars__gnomad_nuclear__cli__query__test__smoke_query_exomes_range_find_all_chr1@exomes-grch37-2.1.snap => annonars__gnomad_nuclear__cli__query__test__smoke_query_range_find_all_chr1@exomes-grch37-2.1.snap} (100%) create mode 100644 src/gnomad_nuclear/cli/snapshots/annonars__gnomad_nuclear__cli__query__test__smoke_query_range_find_all_chr1@exomes-grch38-4.0.snap create mode 100644 src/gnomad_nuclear/cli/snapshots/annonars__gnomad_nuclear__cli__query__test__smoke_query_range_find_all_chr1@genomes-grch38-4.0.snap rename src/gnomad_nuclear/cli/snapshots/{annonars__gnomad_nuclear__cli__query__test__smoke_query_exomes_range_find_first@exomes-grch37-2.1.snap => annonars__gnomad_nuclear__cli__query__test__smoke_query_range_find_first@exomes-grch37-2.1.snap} (100%) create mode 100644 src/gnomad_nuclear/cli/snapshots/annonars__gnomad_nuclear__cli__query__test__smoke_query_range_find_first@exomes-grch38-4.0.snap create mode 100644 src/gnomad_nuclear/cli/snapshots/annonars__gnomad_nuclear__cli__query__test__smoke_query_range_find_first@genomes-grch38-4.0.snap create mode 100644 src/gnomad_nuclear/cli/snapshots/annonars__gnomad_nuclear__cli__query__test__smoke_query_range_find_none_larger@exomes-grch37-2.1.snap create mode 100644 src/gnomad_nuclear/cli/snapshots/annonars__gnomad_nuclear__cli__query__test__smoke_query_range_find_none_larger@exomes-grch38-4.0.snap create mode 100644 src/gnomad_nuclear/cli/snapshots/annonars__gnomad_nuclear__cli__query__test__smoke_query_range_find_none_larger@genomes-grch38-4.0.snap create mode 100644 src/gnomad_nuclear/cli/snapshots/annonars__gnomad_nuclear__cli__query__test__smoke_query_range_find_none_smaller@exomes-grch37-2.1.snap create mode 100644 src/gnomad_nuclear/cli/snapshots/annonars__gnomad_nuclear__cli__query__test__smoke_query_range_find_none_smaller@exomes-grch38-4.0.snap create mode 100644 src/gnomad_nuclear/cli/snapshots/annonars__gnomad_nuclear__cli__query__test__smoke_query_range_find_none_smaller@genomes-grch38-4.0.snap rename src/gnomad_nuclear/cli/snapshots/{annonars__gnomad_nuclear__cli__query__test__smoke_query_exomes_range_find_second@exomes-grch37-2.1.snap => annonars__gnomad_nuclear__cli__query__test__smoke_query_range_find_second@exomes-grch37-2.1.snap} (100%) create mode 100644 src/gnomad_nuclear/cli/snapshots/annonars__gnomad_nuclear__cli__query__test__smoke_query_range_find_second@exomes-grch38-4.0.snap create mode 100644 src/gnomad_nuclear/cli/snapshots/annonars__gnomad_nuclear__cli__query__test__smoke_query_range_find_second@genomes-grch38-4.0.snap rename src/gnomad_nuclear/cli/snapshots/{annonars__gnomad_nuclear__cli__query__test__smoke_query_exomes_var_single@exomes-grch37-2.1.snap => annonars__gnomad_nuclear__cli__query__test__smoke_query_var_single@exomes-grch37-2.1.snap} (100%) create mode 100644 src/gnomad_nuclear/cli/snapshots/annonars__gnomad_nuclear__cli__query__test__smoke_query_var_single@exomes-grch38-4.0.snap create mode 100644 src/gnomad_nuclear/cli/snapshots/annonars__gnomad_nuclear__cli__query__test__smoke_query_var_single@genomes-grch38-4.0.snap diff --git a/src/gnomad_nuclear/cli/import.rs b/src/gnomad_nuclear/cli/import.rs index a105c0e3..7d57d4ab 100644 --- a/src/gnomad_nuclear/cli/import.rs +++ b/src/gnomad_nuclear/cli/import.rs @@ -25,9 +25,9 @@ pub enum GnomadKind { Genomes, } -impl Into for GnomadKind { - fn into(self) -> crate::pbs::gnomad::gnomad4::RecordType { - match self { +impl From for crate::pbs::gnomad::gnomad4::RecordType { + fn from(val: GnomadKind) -> Self { + match val { GnomadKind::Exomes => crate::pbs::gnomad::gnomad4::RecordType::Exomes, GnomadKind::Genomes => crate::pbs::gnomad::gnomad4::RecordType::Genomes, } @@ -414,7 +414,7 @@ pub fn run(common: &common::cli::Args, args: &Args) -> Result<(), anyhow::Error> for (header_field, val) in more_header_values { db.put_cf( &cf_meta, - &format!("gnomad-{}", header_field.replace("_", "-")), + &format!("gnomad-{}", header_field.replace('_', "-")), &val, )?; } @@ -504,7 +504,7 @@ mod test { } #[test] - fn smoke_test_import_gnomad_exomes_grch38() -> Result<(), anyhow::Error> { + fn smoke_test_import_gnomad_exomes_grch38_v2_1() -> Result<(), anyhow::Error> { let tmp_dir = TempDir::default(); let common = common::cli::Args { verbose: Verbosity::new(1, 0), @@ -529,7 +529,7 @@ mod test { } #[test] - fn smoke_test_import_gnomad_genomes_grch38() -> Result<(), anyhow::Error> { + fn smoke_test_import_gnomad_genomes_grch38_v3_1() -> Result<(), anyhow::Error> { let tmp_dir = TempDir::default(); let common = common::cli::Args { verbose: Verbosity::new(1, 0), @@ -552,4 +552,54 @@ mod test { run(&common, &args) } + + #[test] + fn smoke_test_import_gnomad_exomes_grch38_v4_0() -> Result<(), anyhow::Error> { + let tmp_dir = TempDir::default(); + let common = common::cli::Args { + verbose: Verbosity::new(1, 0), + }; + let args = Args { + genome_release: common::cli::GenomeRelease::Grch38, + path_in_vcf: vec![String::from( + "tests/gnomad-nuclear/example-exomes-grch38/v4.0/gnomad-exomes.vcf.bgz", + )], + path_out_rocksdb: format!("{}", tmp_dir.join("out-rocksdb").display()), + cf_name: String::from("gnomad_nuclear_data"), + path_wal_dir: None, + tbi_window_size: 1_000_000, + import_fields_json: Some(serde_json::to_string( + &gnomad3::DetailsOptions::with_all_enabled(), + )?), + gnomad_kind: GnomadKind::Exomes, + gnomad_version: String::from("4.0"), + }; + + run(&common, &args) + } + + #[test] + fn smoke_test_import_gnomad_genomes_grch38_v4_0() -> Result<(), anyhow::Error> { + let tmp_dir = TempDir::default(); + let common = common::cli::Args { + verbose: Verbosity::new(1, 0), + }; + let args = Args { + genome_release: common::cli::GenomeRelease::Grch38, + path_in_vcf: vec![String::from( + "tests/gnomad-nuclear/example-genomes-grch38/v4.0/gnomad-genomes.vcf.bgz", + )], + path_out_rocksdb: format!("{}", tmp_dir.join("out-rocksdb").display()), + cf_name: String::from("gnomad_nuclear_data"), + path_wal_dir: None, + tbi_window_size: 1_000_000, + import_fields_json: Some(serde_json::to_string( + &gnomad3::DetailsOptions::with_all_enabled(), + )?), + gnomad_kind: GnomadKind::Genomes, + gnomad_version: String::from("4.0"), + }; + + run(&common, &args) + } } diff --git a/src/gnomad_nuclear/cli/query.rs b/src/gnomad_nuclear/cli/query.rs index 773981c3..fd1ba75a 100644 --- a/src/gnomad_nuclear/cli/query.rs +++ b/src/gnomad_nuclear/cli/query.rs @@ -291,8 +291,9 @@ mod test { #[rstest::rstest] #[case("exomes", "grch37", "2.1")] - // #[case("exomes", "grch38", "4.0")] - fn smoke_query_exomes_all( + #[case("exomes", "grch38", "4.0")] + #[case("genomes", "grch38", "4.0")] + fn smoke_query_all( #[case] kind: &str, #[case] genome_release: &str, #[case] version: &str, @@ -316,7 +317,9 @@ mod test { #[rstest::rstest] #[case("exomes", "grch37", "2.1")] - fn smoke_query_exomes_var_single( + #[case("exomes", "grch38", "4.0")] + #[case("genomes", "grch38", "4.0")] + fn smoke_query_var_single( #[case] kind: &str, #[case] genome_release: &str, #[case] version: &str, @@ -324,7 +327,14 @@ mod test { crate::common::set_snapshot_suffix!("{}-{}-{}", kind, genome_release, version); let (common, args, _temp) = build_args( ArgsQuery { - variant: Some(spdi::Var::from_str("GRCh37:1:55516888:G:GA")?), + variant: Some(spdi::Var::from_str(&format!( + "{}:1:55516888:G:GA", + if genome_release == "grch37" { + "GRCh37" + } else { + "GRCh38" + } + ))?), ..Default::default() }, kind, @@ -340,7 +350,9 @@ mod test { #[rstest::rstest] #[case("exomes", "grch37", "2.1")] - fn smoke_query_exomes_pos_single( + #[case("exomes", "grch38", "4.0")] + #[case("genomes", "grch38", "4.0")] + fn smoke_query_pos_single( #[case] kind: &str, #[case] genome_release: &str, #[case] version: &str, @@ -348,7 +360,14 @@ mod test { crate::common::set_snapshot_suffix!("{}-{}-{}", kind, genome_release, version); let (common, args, _temp) = build_args( ArgsQuery { - position: Some(spdi::Pos::from_str("GRCh37:1:55516888")?), + position: Some(spdi::Pos::from_str(&format!( + "{}:1:55516888", + if genome_release == "grch37" { + "GRCh37" + } else { + "GRCh38" + } + ))?), ..Default::default() }, kind, @@ -364,7 +383,9 @@ mod test { #[rstest::rstest] #[case("exomes", "grch37", "2.1")] - fn smoke_query_exomes_range_find_all_chr1( + #[case("exomes", "grch38", "4.0")] + #[case("genomes", "grch38", "4.0")] + fn smoke_query_range_find_all_chr1( #[case] kind: &str, #[case] genome_release: &str, #[case] version: &str, @@ -372,7 +393,14 @@ mod test { crate::common::set_snapshot_suffix!("{}-{}-{}", kind, genome_release, version); let (common, args, _temp) = build_args( ArgsQuery { - range: Some(spdi::Range::from_str("GRCh37:1:1:249250621")?), + range: Some(spdi::Range::from_str(&format!( + "{}:1:1:249250621", + if genome_release == "grch37" { + "GRCh37" + } else { + "GRCh38" + } + ))?), ..Default::default() }, kind, @@ -388,7 +416,9 @@ mod test { #[rstest::rstest] #[case("exomes", "grch37", "2.1")] - fn smoke_query_exomes_range_find_first( + #[case("exomes", "grch38", "4.0")] + #[case("genomes", "grch38", "4.0")] + fn smoke_query_range_find_first( #[case] kind: &str, #[case] genome_release: &str, #[case] version: &str, @@ -396,7 +426,14 @@ mod test { crate::common::set_snapshot_suffix!("{}-{}-{}", kind, genome_release, version); let (common, args, _temp) = build_args( ArgsQuery { - range: Some(spdi::Range::from_str("GRCh37:1:55505599:55505599")?), + range: Some(spdi::Range::from_str(&format!( + "{}:1:55505599:55505599", + if genome_release == "grch37" { + "GRCh37" + } else { + "GRCh38" + } + ))?), ..Default::default() }, kind, @@ -412,7 +449,9 @@ mod test { #[rstest::rstest] #[case("exomes", "grch37", "2.1")] - fn smoke_query_exomes_range_find_second( + #[case("exomes", "grch38", "4.0")] + #[case("genomes", "grch38", "4.0")] + fn smoke_query_range_find_second( #[case] kind: &str, #[case] genome_release: &str, #[case] version: &str, @@ -420,7 +459,14 @@ mod test { crate::common::set_snapshot_suffix!("{}-{}-{}", kind, genome_release, version); let (common, args, _temp) = build_args( ArgsQuery { - range: Some(spdi::Range::from_str("GRCh37:1:55505615:55505615")?), + range: Some(spdi::Range::from_str(&format!( + "{}:1:55505615:55505615", + if genome_release == "grch37" { + "GRCh37" + } else { + "GRCh38" + } + ))?), ..Default::default() }, kind, @@ -436,7 +482,9 @@ mod test { #[rstest::rstest] #[case("exomes", "grch37", "2.1")] - fn smoke_query_exomes_range_find_none_smaller( + #[case("exomes", "grch38", "4.0")] + #[case("genomes", "grch38", "4.0")] + fn smoke_query_range_find_none_smaller( #[case] kind: &str, #[case] genome_release: &str, #[case] version: &str, @@ -444,7 +492,14 @@ mod test { crate::common::set_snapshot_suffix!("{}-{}-{}", kind, genome_release, version); let (common, args, _temp) = build_args( ArgsQuery { - range: Some(spdi::Range::from_str("GRCh37:1:1:55505598")?), + range: Some(spdi::Range::from_str(&format!( + "{}:1:1:55505598", + if genome_release == "grch37" { + "GRCh37" + } else { + "GRCh38" + } + ))?), ..Default::default() }, kind, @@ -460,7 +515,9 @@ mod test { #[rstest::rstest] #[case("exomes", "grch37", "2.1")] - fn smoke_query_exomes_range_find_none_larger( + #[case("exomes", "grch38", "4.0")] + #[case("genomes", "grch38", "4.0")] + fn smoke_query_range_find_none_larger( #[case] kind: &str, #[case] genome_release: &str, #[case] version: &str, @@ -468,7 +525,14 @@ mod test { crate::common::set_snapshot_suffix!("{}-{}-{}", kind, genome_release, version); let (common, args, _temp) = build_args( ArgsQuery { - range: Some(spdi::Range::from_str("GRCh37:1:55516889:249250621")?), + range: Some(spdi::Range::from_str(&format!( + "{}:1:55516889:249250621", + if genome_release == "grch37" { + "GRCh37" + } else { + "GRCh38" + } + ))?), ..Default::default() }, kind, diff --git a/src/gnomad_nuclear/cli/snapshots/annonars__gnomad_nuclear__cli__query__test__smoke_query_exomes_all@exomes-grch37-2.1.snap b/src/gnomad_nuclear/cli/snapshots/annonars__gnomad_nuclear__cli__query__test__smoke_query_all@exomes-grch37-2.1.snap similarity index 100% rename from src/gnomad_nuclear/cli/snapshots/annonars__gnomad_nuclear__cli__query__test__smoke_query_exomes_all@exomes-grch37-2.1.snap rename to src/gnomad_nuclear/cli/snapshots/annonars__gnomad_nuclear__cli__query__test__smoke_query_all@exomes-grch37-2.1.snap diff --git a/src/gnomad_nuclear/cli/snapshots/annonars__gnomad_nuclear__cli__query__test__smoke_query_all@exomes-grch38-4.0.snap b/src/gnomad_nuclear/cli/snapshots/annonars__gnomad_nuclear__cli__query__test__smoke_query_all@exomes-grch38-4.0.snap new file mode 100644 index 00000000..09836a69 --- /dev/null +++ b/src/gnomad_nuclear/cli/snapshots/annonars__gnomad_nuclear__cli__query__test__smoke_query_all@exomes-grch38-4.0.snap @@ -0,0 +1,11 @@ +--- +source: 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