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update validator to value_parser
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Rob Patro committed Jul 14, 2022
1 parent ee41561 commit b23d4ef
Showing 1 changed file with 42 additions and 30 deletions.
72 changes: 42 additions & 30 deletions src/main.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -46,28 +46,28 @@ fn gen_random_kmer(k: usize) -> String {
/// any valid entity (e.g. disk file, FIFO, directory, etc.).
/// If there is any issue with permissions or failure to properly
/// resolve symlinks, or if the path is wrong, it returns
/// an Err(String), else Ok(()).
fn file_exists_validator(v: &str) -> Result<(), String> {
/// an Err(String), else Ok(String).
fn file_exists_validator(v: &str) -> Result<String, String> {
// NOTE: we explicitly *do not* check `is_file()` here
// since we want to return true even if the path is to
// a FIFO/named pipe.
if !Path::new(v).exists() {
Err(String::from("No valid file was found at this path."))
} else {
Ok(())
Ok(v.to_string())
}
}

/// Checks if the path pointed to by v exists and is
/// a valid directory on disk. If there is any issue
/// with permissions or failure to properly
/// resolve symlinks, or if the path is wrong, it returns
/// an Err(String), else Ok(()).
fn directory_exists_validator(v: &str) -> Result<(), String> {
/// an Err(String), else Ok(String).
fn directory_exists_validator(v: &str) -> Result<String, String> {
if !Path::new(v).is_dir() {
Err(String::from("No valid directory was found at this path."))
} else {
Ok(())
Ok(v.to_string())
}
}

Expand All @@ -86,7 +86,7 @@ fn main() -> anyhow::Result<()> {
.about("Convert a BAM file to a RAD file")
.version(version)
.author(crate_authors)
.arg(arg!(-b --bam <BAMFILE> "input SAM/BAM file").validator(file_exists_validator))
.arg(arg!(-b --bam <BAMFILE> "input SAM/BAM file").value_parser(file_exists_validator))
.arg(
arg!(-t --threads <THREADS> "number of threads to use for processing")
.value_parser(value_parser!(u32))
Expand All @@ -98,7 +98,7 @@ fn main() -> anyhow::Result<()> {
.about("View a RAD file")
.version(version)
.author(crate_authors)
.arg(arg!(-r --rad <RADFILE> "input RAD file").validator(file_exists_validator))
.arg(arg!(-r --rad <RADFILE> "input RAD file").value_parser(file_exists_validator))
.arg(
arg!(-H --header "flag for printing header")
.takes_value(false)
Expand All @@ -111,8 +111,10 @@ fn main() -> anyhow::Result<()> {
.version(version)
.author(crate_authors)
.arg(arg!(-i --input <INPUT> "input directory containing the map.rad RAD file")
.validator(directory_exists_validator))
.arg(arg!(-d --"expected-ori" <EXPECTEDORI> "the expected orientation of alignments"))
.value_parser(directory_exists_validator))
.arg(arg!(-d --"expected-ori" <EXPECTEDORI> "the expected orientation of alignments")
.ignore_case(true)
.value_parser(["fw", "rc", "both", "either"]))
.arg(arg!(-o --"output-dir" <OUTPUTDIR> "output directory"))
.arg(arg!(
-k --"knee-distance" "attempt to determine the number of barcodes to keep using the knee distance method."
Expand All @@ -126,12 +128,14 @@ fn main() -> anyhow::Result<()> {
)
.arg(
arg!(-b --"valid-bc" <VALIDBC> "uses true barcode collected from a provided file")
.conflicts_with_all(&["force-cells", "expect-cells", "knee-distance", "unfiltered-pl"]),
.conflicts_with_all(&["force-cells", "expect-cells", "knee-distance", "unfiltered-pl"])
.value_parser(file_exists_validator)
)
.arg(
arg!(-u --"unfiltered-pl" <UNFILTEREDPL> "uses an unfiltered external permit list")
.conflicts_with_all(&["force-cells", "expect-cells", "knee-distance", "valid-bc"])
.requires("min-reads")
.value_parser(file_exists_validator)
)
.arg(
arg!(-m --"min-reads" <MINREADS> "minimum read count threshold; only used with --unfiltered-pl")
Expand All @@ -146,24 +150,22 @@ fn main() -> anyhow::Result<()> {
.version(version)
.author(crate_authors)
.arg(arg!(-i --"input-dir" <INPUTDIR> "input directory made by generate-permit-list")
.validator(directory_exists_validator))
.value_parser(directory_exists_validator))
.arg(arg!(-r --"rad-dir" <RADFILE> "the directory containing the RAD file to be collated")
.validator(directory_exists_validator))
.value_parser(directory_exists_validator))
.arg(arg!(-t --threads <THREADS> "number of threads to use for processing").value_parser(value_parser!(u32)).default_value(&max_num_collate_threads))
.arg(arg!(-c --compress "compress the output collated RAD file").takes_value(false).required(false))
.arg(arg!(-m --"max-records" <MAXRECORDS> "the maximum number of read records to keep in memory at once")
.value_parser(value_parser!(u32))
.default_value("30000000"));
//.arg(arg!(-e --expected-ori=[expected-ori] 'the expected orientation of alignments'")
// .default_value(fw"));

let quant_app = Command::new("quant")
.about("Quantify expression from a collated RAD file")
.version(version)
.author(crate_authors)
.arg(arg!(-i --"input-dir" <INPUTDIR> "input directory containing collated RAD file")
.validator(directory_exists_validator))
.arg(arg!(-m --"tg-map" <TGMAP> "transcript to gene map").validator(file_exists_validator))
.value_parser(directory_exists_validator))
.arg(arg!(-m --"tg-map" <TGMAP> "transcript to gene map").value_parser(file_exists_validator))
.arg(arg!(-o --"output-dir" <OUTPUTDIR> "output directory where quantification results will be written"))
.arg(arg!(-t --threads <THREADS> "number of threads to use for processing").value_parser(value_parser!(u32)).default_value(&max_num_threads))
.arg(arg!(-d --"dump-eqclasses" "flag for dumping equivalence classes").takes_value(false).required(false))
Expand All @@ -172,16 +174,17 @@ fn main() -> anyhow::Result<()> {
.arg(arg!(--"summary-stat" "flag for storing only summary statistics").requires("num-bootstraps").takes_value(false).required(false))
.arg(arg!(--"use-mtx" "flag for writing output matrix in matrix market format (default)").takes_value(false).required(false))
.arg(arg!(--"use-eds" "flag for writing output matrix in EDS format").takes_value(false).required(false).conflicts_with("use-mtx"))
.arg(arg!(--"quant-subset" <SFILE> "file containing list of barcodes to quantify, those not in this list will be ignored").required(false))
.arg(arg!(--"quant-subset" <SFILE> "file containing list of barcodes to quantify, those not in this list will be ignored").required(false).value_parser(file_exists_validator))
.arg(arg!(-r --resolution <RESOLUTION> "the resolution strategy by which molecules will be counted")
.ignore_case(true)
.value_parser(["full", "trivial", "cr-like", "cr-like-em", "parsimony", "parsimony-em", "parsimony-gene", "parsimony-gene-em"]))
.ignore_case(true)
.value_parser(["full", "trivial", "cr-like", "cr-like-em", "parsimony", "parsimony-em", "parsimony-gene", "parsimony-gene-em"]))
.arg(arg!(--"sa-model" "preferred model of splicing ambiguity")
.ignore_case(true)
.value_parser(["prefer-ambig", "winner-take-all"])
.default_value("winner-take-all")
.hide(true))
.arg(arg!(--"umi-edit-dist" <EDIST> "the Hamming distance within which potentially colliding UMIs will be considered for correction")
.value_parser(value_parser!(u32))
.value_parser(value_parser!(u32))
.default_value_ifs(&[
("resolution", Some("cr-like"), Some("0")),
("resolution", Some("cr-like-em"), Some("0")),
Expand All @@ -195,7 +198,7 @@ fn main() -> anyhow::Result<()> {
.required(false)
.hide(true))
.arg(arg!(--"large-graph-thresh" <NVERT> "the order (number of nodes) of a PUG above which the alternative resolution strategy will be applied")
.value_parser(value_parser!(usize))
.value_parser(value_parser!(usize))
.default_value_ifs(&[
("resolution", Some("parsimony-gene-em"), Some("1000")),
("resolution", Some("parsimony"), Some("1000")),
Expand All @@ -207,23 +210,23 @@ fn main() -> anyhow::Result<()> {
.required(false)
.hide(true))
.arg(arg!(--"small-thresh" <SMALLTHRESH> "cells with fewer than these many reads will be resolved using a custom approach")
.value_parser(value_parser!(usize))
.default_value("10")
.value_parser(value_parser!(usize))
.default_value("10")
.hide(true));

let infer_app = Command::new("infer")
.about("Perform inference on equivalence class count data")
.version(version)
.author(crate_authors)
.arg(arg!(-c --"count-mat" <EQCMAT> "matrix of cells by equivalence class counts")
.validator(file_exists_validator).takes_value(true).required(true))
.value_parser(file_exists_validator).takes_value(true).required(true))
//.arg(arg!(-b --barcodes=<barcodes> "file containing the barcodes labeling the matrix rows").takes_value(true).required(true))
.arg(arg!(-e --"eq-labels" <EQLABELS> "file containing the gene labels of the equivalence classes")
.validator(file_exists_validator).takes_value(true).required(true))
.value_parser(file_exists_validator).takes_value(true).required(true))
.arg(arg!(-o --"output-dir" <OUTPUTDIR> "output directory where quantification results will be written").takes_value(true).required(true))
.arg(arg!(-t --threads <THREADS> "number of threads to use for processing").value_parser(value_parser!(u32)).default_value(&max_num_threads))
.arg(arg!(--usa "flag specifying that input equivalence classes were computed in USA mode").takes_value(false).required(false))
.arg(arg!(--"quant-subset" <SFILE> "file containing list of barcodes to quantify, those not in this list will be ignored").required(false))
.arg(arg!(--"quant-subset" <SFILE> "file containing list of barcodes to quantify, those not in this list will be ignored").required(false).value_parser(file_exists_validator))
.arg(arg!(--"use-mtx" "flag for writing output matrix in matrix market format (default)").takes_value(false).required(false))
.arg(arg!(--"use-eds" "flag for writing output matrix in EDS format").takes_value(false).required(false).conflicts_with("use-mtx"));

Expand Down Expand Up @@ -257,13 +260,22 @@ fn main() -> anyhow::Result<()> {
// You can handle information about subcommands by requesting their matches by name
// (as below), requesting just the name used, or both at the same time
if let Some(t) = opts.subcommand_matches("generate-permit-list") {
let input_dir: String = t.get_one::<String>("input").expect("no input directory specified").to_string();
let input_dir: String = t
.get_one::<String>("input")
.expect("no input directory specified")
.to_string();
let output_dir: String = t
.get_one::<String>("output-dir")
.expect("no input directory specified").to_string();
.expect("no input directory specified")
.to_string();

let valid_ori: bool;
let expected_ori = match t.get_one::<String>("expected-ori").unwrap().to_uppercase().as_str() {
let expected_ori = match t
.get_one::<String>("expected-ori")
.unwrap()
.to_uppercase()
.as_str()
{
"RC" => {
valid_ori = true;
Strand::Reverse
Expand Down

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