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Fix a bunch more clippy lints.
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@macklin-10x
macklin-10x committed Feb 22, 2024
1 parent dc703e0 commit 7f79057
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Showing 2 changed files with 67 additions and 90 deletions.
83 changes: 35 additions & 48 deletions vdj_ann_ref/src/bin/build_vdj_ref.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -146,10 +146,7 @@ fn header_from_gene(gene: &str, is_utr: bool, record: &mut usize, source: &str)
} else {
region_type = format!("{}-REGION", genev[3] as char);
}
format!(
"{}|{} {}|{}|{}|{}",
record, gene, source, gene, region_type, header_tail
)
format!("{record}|{gene} {source}|{gene}|{region_type}|{header_tail}")
}

fn print_fasta<R: Write>(out: &mut R, header: &str, seq: &DnaStringSlice, none: bool) {
Expand Down Expand Up @@ -196,7 +193,7 @@ fn add_gene<R: Write>(
return;
}
if !to_chr.contains_key(&chr.to_string()) {
eprintln!("gene = {}, chr = {}", gene, chr);
eprintln!("gene = {gene}, chr = {chr}");
}
let chrid = to_chr[chr];
let seq = refs[chrid].slice(start - 1, stop);
Expand Down Expand Up @@ -413,7 +410,7 @@ fn main() {
// Define root output directory.

let root = "vdj_ann_ref/vdj_refs";
let mut out = open_for_write_new![&format!("{}/{}/fasta/regions.fa", root, species)];
let mut out = open_for_write_new![&format!("{root}/{species}/fasta/regions.fa")];

// Define release. If this is ever changed, the effect on the fasta output
// files should be very carefully examined. Specify sequence source.
Expand All @@ -422,15 +419,15 @@ fn main() {
let version = "7.0.0";
let (source, source2) = match species {
"human" => (
format!("GRCh38-release{}", release),
format!("GRCh38-release{release}"),
"vdj_GRCh38_alts_ensembl".to_string(),
),
"mouse" => (
format!("GRCm38-release{}", release),
format!("GRCm38-release{release}"),
"vdj_GRCm38_alts_ensembl".to_string(),
),
_ => {
let source = format!("BALB_cJ_v1.{}", release);
let source = format!("BALB_cJ_v1.{release}");
(source.clone(), source)
}
};
Expand Down Expand Up @@ -895,7 +892,6 @@ fn main() {
// End mouse changes for cell ranger 5.0.
// ▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓
}
if species == "balbc" {}

// Normalize exceptions.

Expand All @@ -918,47 +914,38 @@ fn main() {
"balbc" => "mus_musculus_balbcj",
_ => "",
};
let releasep = format!("release-{}", release);
let releasep = format!("release-{release}");
let csn = cap1(species_name);
match (species, ftype) {
("mouse", "gff3") => format!(
"{}/{}/{}/{}.GRCm38.{}.gff3",
releasep, ftype, species_name, csn, release
),
("mouse", "gtf") => format!(
"{}/{}/{}/{}.GRCm38.{}.gtf",
releasep, ftype, species_name, csn, release
),
("mouse", "fasta") => format!(
"{}/{}/{}/dna/{}.GRCm38.dna.toplevel.fa",
releasep, ftype, species_name, csn
),
("mouse", "gff3") => {
format!("{releasep}/{ftype}/{species_name}/{csn}.GRCm38.{release}.gff3")
}
("mouse", "gtf") => {
format!("{releasep}/{ftype}/{species_name}/{csn}.GRCm38.{release}.gtf")
}
("mouse", "fasta") => {
format!("{releasep}/{ftype}/{species_name}/dna/{csn}.GRCm38.dna.toplevel.fa")
}

("balbc", "gff3") => format!(
"{}/{}/{}/{}.BALB_cJ_v1.{}.gff3",
releasep, ftype, species_name, csn, release
),
("balbc", "gtf") => format!(
"{}/{}/{}/{}.BALB_cJ_v1.{}.gtf",
releasep, ftype, species_name, csn, release
),
("balbc", "fasta") => format!(
"{}/{}/{}/dna/{}.BALB_cJ_v1.dna.toplevel.fa",
releasep, ftype, species_name, csn
),
("balbc", "gff3") => {
format!("{releasep}/{ftype}/{species_name}/{csn}.BALB_cJ_v1.{release}.gff3")
}
("balbc", "gtf") => {
format!("{releasep}/{ftype}/{species_name}/{csn}.BALB_cJ_v1.{release}.gtf")
}
("balbc", "fasta") => {
format!("{releasep}/{ftype}/{species_name}/dna/{csn}.BALB_cJ_v1.dna.toplevel.fa")
}

("human", "gff3") => format!(
"{}/{}/{}/{}.GRCh38.{}.chr_patch_hapl_scaff.gff3",
releasep, ftype, species_name, csn, release
"{releasep}/{ftype}/{species_name}/{csn}.GRCh38.{release}.chr_patch_hapl_scaff.gff3"
),
("human", "gtf") => format!(
"{}/{}/{}/{}.GRCh38.{}.chr_patch_hapl_scaff.gtf",
releasep, ftype, species_name, csn, release
),
("human", "fasta") => format!(
"{}/{}/{}/dna/{}.GRCh38.dna.toplevel.fa",
releasep, ftype, species_name, csn
"{releasep}/{ftype}/{species_name}/{csn}.GRCh38.{release}.chr_patch_hapl_scaff.gtf"
),
("human", "fasta") => {
format!("{releasep}/{ftype}/{species_name}/dna/{csn}.GRCh38.dna.toplevel.fa")
}
_ => String::default(),
}
}
Expand All @@ -972,16 +959,16 @@ fn main() {

if download {
fn fetch(species: &str, ftype: &str, release: i32) {
println!("fetching {}.{}", species, ftype);
println!("fetching {species}.{ftype}");
let path = ensembl_path(species, ftype, release);
let external = "ftp://ftp.ensembl.org/pub";
let internal = "/mnt/opt/meowmix_git/ensembl";
let dir = format!("{}/{}", internal, path.rev_before("/"));
fs::create_dir_all(&dir).unwrap();
let full_path = format!("{}/{}", internal, path);
let full_path = format!("{internal}/{path}");
Command::new("wget")
.current_dir(&dir)
.arg(format!("{}/{}.gz", external, path))
.arg(format!("{external}/{path}.gz"))
.status()
.expect("wget failed");
if ftype != "fasta" {
Expand Down Expand Up @@ -1023,7 +1010,7 @@ fn main() {

// Generate reference.json. Note version number.

let mut json = open_for_write_new![&format!("{}/{}/reference.json", root, species)];
let mut json = open_for_write_new![&format!("{root}/{species}/reference.json")];
fwriteln!(json, "{{");
let mut sha256 = Sha256::new();
copy(&mut File::open(&fasta).unwrap(), &mut sha256).unwrap();
Expand Down Expand Up @@ -1158,7 +1145,7 @@ fn main() {
]
.iter()
{
gene2 = gene2.replace(&format!("{} ", x), &x[0..1].to_uppercase());
gene2 = gene2.replace(&format!("{x} "), &x[0..1].to_uppercase());
}

// More fixing.
Expand Down
74 changes: 32 additions & 42 deletions vdj_ann_ref/src/bin/build_vdj_ref_exons.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -211,9 +211,9 @@ fn main() {
let version = "4.0.0";
let source2: String;
if species == "human" {
source2 = format!("vdj_GRCh38_alts_ensembl-{}", version);
source2 = format!("vdj_GRCh38_alts_ensembl-{version}");
} else if species == "mouse" {
source2 = format!("vdj_GRCm38_alts_ensembl-{}", version);
source2 = format!("vdj_GRCm38_alts_ensembl-{version}");
} else {
source2 = String::new();
}
Expand Down Expand Up @@ -532,7 +532,6 @@ fn main() {

left_trims.push(("IGLC2", 1));
}
if species == "balbc" {}

// Normalize exceptions.

Expand All @@ -555,47 +554,38 @@ fn main() {
"balbc" => "mus_musculus_balbcj",
_ => "",
};
let releasep = format!("release-{}", release);
let releasep = format!("release-{release}");
let csn = cap1(species_name);
match (species, ftype) {
("mouse", "gff3") => format!(
"{}/{}/{}/{}.GRCm38.{}.gff3",
releasep, ftype, species_name, csn, release
),
("mouse", "gtf") => format!(
"{}/{}/{}/{}.GRCm38.{}.gtf",
releasep, ftype, species_name, csn, release
),
("mouse", "fasta") => format!(
"{}/{}/{}/dna/{}.GRCm38.dna.toplevel.fa",
releasep, ftype, species_name, csn
),
("mouse", "gff3") => {
format!("{releasep}/{ftype}/{species_name}/{csn}.GRCm38.{release}.gff3")
}
("mouse", "gtf") => {
format!("{releasep}/{ftype}/{species_name}/{csn}.GRCm38.{release}.gtf")
}
("mouse", "fasta") => {
format!("{releasep}/{ftype}/{species_name}/dna/{csn}.GRCm38.dna.toplevel.fa")
}

("balbc", "gff3") => format!(
"{}/{}/{}/{}.BALB_cJ_v1.{}.gff3",
releasep, ftype, species_name, csn, release
),
("balbc", "gtf") => format!(
"{}/{}/{}/{}.BALB_cJ_v1.{}.gtf",
releasep, ftype, species_name, csn, release
),
("balbc", "fasta") => format!(
"{}/{}/{}/dna/{}.BALB_cJ_v1.dna.toplevel.fa",
releasep, ftype, species_name, csn
),
("balbc", "gff3") => {
format!("{releasep}/{ftype}/{species_name}/{csn}.BALB_cJ_v1.{release}.gff3")
}
("balbc", "gtf") => {
format!("{releasep}/{ftype}/{species_name}/{csn}.BALB_cJ_v1.{release}.gtf")
}
("balbc", "fasta") => {
format!("{releasep}/{ftype}/{species_name}/dna/{csn}.BALB_cJ_v1.dna.toplevel.fa")
}

("human", "gff3") => format!(
"{}/{}/{}/{}.GRCh38.{}.chr_patch_hapl_scaff.gff3",
releasep, ftype, species_name, csn, release
"{releasep}/{ftype}/{species_name}/{csn}.GRCh38.{release}.chr_patch_hapl_scaff.gff3"
),
("human", "gtf") => format!(
"{}/{}/{}/{}.GRCh38.{}.chr_patch_hapl_scaff.gtf",
releasep, ftype, species_name, csn, release
),
("human", "fasta") => format!(
"{}/{}/{}/dna/{}.GRCh38.dna.toplevel.fa",
releasep, ftype, species_name, csn
"{releasep}/{ftype}/{species_name}/{csn}.GRCh38.{release}.chr_patch_hapl_scaff.gtf"
),
("human", "fasta") => {
format!("{releasep}/{ftype}/{species_name}/dna/{csn}.GRCh38.dna.toplevel.fa")
}
_ => String::new(),
}
}
Expand All @@ -609,16 +599,16 @@ fn main() {

if download {
fn fetch(species: &str, ftype: &str, release: i32) {
println!("fetching {}.{}", species, ftype);
println!("fetching {species}.{ftype}");
let path = ensembl_path(species, ftype, release);
let external = "ftp://ftp.ensembl.org/pub";
let internal = "/mnt/opt/meowmix_git/ensembl";
let dir = format!("{}/{}", internal, path.rev_before("/"));
fs::create_dir_all(&dir).unwrap();
let full_path = format!("{}/{}", internal, path);
let full_path = format!("{internal}/{path}");
Command::new("wget")
.current_dir(&dir)
.arg(format!("{}/{}.gz", external, path))
.arg(format!("{external}/{path}.gz"))
.status()
.expect("wget failed");
if ftype != "fasta" {
Expand Down Expand Up @@ -660,7 +650,7 @@ fn main() {

// Generate reference.json. Note version number.

let mut json = open_for_write_new![&format!("{}/{}/reference.json", root, species)];
let mut json = open_for_write_new![&format!("{root}/{species}/reference.json")];
fwriteln!(json, "{{");
let mut sha256 = Sha256::new();
copy(&mut File::open(&fasta).unwrap(), &mut sha256).unwrap();
Expand Down Expand Up @@ -795,7 +785,7 @@ fn main() {
]
.iter()
{
gene2 = gene2.replace(&format!("{} ", x), &x[0..1].to_uppercase());
gene2 = gene2.replace(&format!("{x} "), &x[0..1].to_uppercase());
}

// More fixing.
Expand Down Expand Up @@ -972,7 +962,7 @@ fn main() {
} else {
starts[i + 1] - stops[i]
};
print!(", intron = {}", intron);
print!(", intron = {intron}");
}
} else if exons[i].0.as_bytes()[3] == b'V' {
print!(", 5'-UTR");
Expand Down

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