Skip to content

Commit

Permalink
refactor!: remove duplicate name for parsimony-em
Browse files Browse the repository at this point in the history 
To streamline, simplify and robustify parsing, we have
removed the redundant name "full" that could previously
be passed as a resolution mode.  This mode was alway
simply an alias for "parsimony-em". As more resolution
modes have been and are being added, the name "full" for
this mode no longer really makes sense.  Further, "parsimony-em"
is more explicit and a better name for this mode. Moving
forward, "full" will no longer work as an alias for this mode
and will appear as unrecognized.
  • Loading branch information
Rob Patro committed Jul 14, 2022
1 parent 8ea680f commit 23eb300
Show file tree
Hide file tree
Showing 3 changed files with 41 additions and 63 deletions.
1 change: 1 addition & 0 deletions src/lib.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@
*/

pub mod cellfilter;
pub mod cmd_parse_utils;
pub mod collate;
pub mod constants;
pub mod convert;
Expand Down
101 changes: 39 additions & 62 deletions src/main.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -9,16 +9,19 @@

use anyhow::{anyhow, bail};
use bio_types::strand::Strand;
use clap::{arg, crate_authors, crate_version, value_parser, Command};
use clap::{arg, builder::ArgGroup, crate_authors, crate_version, value_parser, Command};
use csv::Error as CSVError;
use csv::ErrorKind;
use itertools::Itertools;
use mimalloc::MiMalloc;
use rand::Rng;
use slog::{crit, o, warn, Drain};
use std::path::{Path, PathBuf};
use std::path::PathBuf;

use alevin_fry::cellfilter::{generate_permit_list, CellFilterMethod};
use alevin_fry::cmd_parse_utils::{
pathbuf_directory_exists_validator, pathbuf_file_exists_validator,
};
use alevin_fry::prog_opts::{GenPermitListOpts, QuantOpts};
use alevin_fry::quant::{ResolutionStrategy, SplicedAmbiguityModel};

Expand All @@ -41,35 +44,6 @@ fn gen_random_kmer(k: usize) -> String {
s
}

/// Checks if the path pointed to by v exists. It can be
/// 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(PathBuf).
fn pathbuf_file_exists_validator(v: &str) -> Result<PathBuf, 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(PathBuf::from(v))
}
}

/// 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(PathBuf).
fn pathbuf_directory_exists_validator(v: &str) -> Result<PathBuf, String> {
if !Path::new(v).is_dir() {
Err(String::from("No valid directory was found at this path."))
} else {
Ok(PathBuf::from(v))
}
}

fn main() -> anyhow::Result<()> {
let num_hardware_threads = num_cpus::get() as u32;
let max_num_threads: String = (num_cpus::get() as u32).to_string();
Expand All @@ -90,7 +64,7 @@ fn main() -> anyhow::Result<()> {
.value_parser(pathbuf_file_exists_validator),
)
.arg(
arg!(-t --threads <THREADS> "number of threads to use for processing")
arg!(-t --threads [THREADS] "number of threads to use for processing")
.value_parser(value_parser!(u32))
.default_value(&max_num_threads),
)
Expand All @@ -106,7 +80,7 @@ fn main() -> anyhow::Result<()> {
.takes_value(false)
.required(false),
)
.arg(arg!(-o --output <RADFILE> "output plain-text-file file").required(false));
.arg(arg!(-o --output [RADFILE] "output plain-text-file file"));

let gen_app = Command::new("generate-permit-list")
.about("Generate a permit list of barcodes from a RAD file")
Expand Down Expand Up @@ -136,16 +110,16 @@ fn main() -> anyhow::Result<()> {
.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(pathbuf_file_exists_validator)
)
.group(ArgGroup::new("filter-method")
.args(&["knee-distance", "expect-cells", "force-cells", "valid-bc", "unfiltered-pl"])
.required(true)
)
.arg(
arg!(-m --"min-reads" <MINREADS> "minimum read count threshold; only used with --unfiltered-pl")
.value_parser(value_parser!(u32))
.default_value("10")
.takes_value(true)
.required(true));
//.arg(Arg::from("-v --velocity-mode 'flag for velocity mode'").takes_value(false).required(false));
arg!(-m --"min-reads" [MINREADS] "minimum read count threshold; only used with --unfiltered-pl")
.value_parser(value_parser!(usize))
.default_value("10"));

let collate_app = Command::new("collate")
.about("Collate a RAD file by corrected cell barcode")
Expand All @@ -155,9 +129,9 @@ fn main() -> anyhow::Result<()> {
.value_parser(pathbuf_directory_exists_validator))
.arg(arg!(-r --"rad-dir" <RADFILE> "the directory containing the RAD file to be collated")
.value_parser(pathbuf_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!(-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")
.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"));

Expand All @@ -169,49 +143,46 @@ fn main() -> anyhow::Result<()> {
.value_parser(pathbuf_directory_exists_validator))
.arg(arg!(-m --"tg-map" <TGMAP> "transcript to gene map").value_parser(pathbuf_file_exists_validator))
.arg(arg!(-o --"output-dir" <OUTPUTDIR> "output directory where quantification results will be written").value_parser(value_parser!(PathBuf)))
.arg(arg!(-t --threads <THREADS> "number of threads to use for processing").value_parser(value_parser!(u32)).default_value(&max_num_threads))
.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))
.arg(arg!(-b --"num-bootstraps" <NUMBOOTSTRAPS> "number of bootstraps to use").value_parser(value_parser!(u32)).default_value("0"))
.arg(arg!(-b --"num-bootstraps" [NUMBOOTSTRAPS] "number of bootstraps to use").value_parser(value_parser!(u32)).default_value("0"))
.arg(arg!(--"init-uniform" "flag for uniform sampling").requires("num-bootstraps").takes_value(false).required(false))
.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).value_parser(pathbuf_file_exists_validator))
.arg(arg!(--"quant-subset" [SFILE] "file containing list of barcodes to quantify, those not in this list will be ignored").value_parser(pathbuf_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"]))
.arg(arg!(--"sa-model" "preferred model of splicing ambiguity")
.value_parser(value_parser!(ResolutionStrategy)))
.arg(arg!(--"sa-model" [SAMODEL] "preferred model of splicing ambiguity")
.ignore_case(true)
.value_parser(["prefer-ambig", "winner-take-all"])
.value_parser(value_parser!(SplicedAmbiguityModel))
.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")
.arg(arg!(--"umi-edit-dist" [EDIST] "the Hamming distance within which potentially colliding UMIs will be considered for correction")
.value_parser(value_parser!(u32))
.default_value_ifs(&[
("resolution", Some("cr-like"), Some("0")),
("resolution", Some("cr-like-em"), Some("0")),
("resolution", Some("trivial"), Some("0")),
("resolution", Some("parsimony"), Some("1")),
("resolution", Some("parsimony-em"), Some("1")),
("resolution", Some("full"), Some("1")),
("resolution", Some("parsimony-gene"), Some("1")),
("resolution", Some("parsimony-gene-em"), Some("1")),
])
.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")
.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))
.default_value_ifs(&[
("resolution", Some("parsimony-gene-em"), Some("1000")),
("resolution", Some("parsimony"), Some("1000")),
("resolution", Some("full"), Some("1000")),
("resolution", Some("parsimony-em"), Some("1000")),
("resolution", Some("parsimony-gene"), Some("1000")),
("resolution", Some("parsimony-gene"), Some("1000")),
])
.default_value("0") // for any other mode
.required(false)
.hide(true))
.arg(arg!(--"small-thresh" <SMALLTHRESH> "cells with fewer than these many reads will be resolved using a custom approach")
.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")
.hide(true));
Expand All @@ -221,14 +192,14 @@ fn main() -> anyhow::Result<()> {
.version(version)
.author(crate_authors)
.arg(arg!(-c --"count-mat" <EQCMAT> "matrix of cells by equivalence class counts")
.value_parser(pathbuf_file_exists_validator).takes_value(true).required(true))
.value_parser(pathbuf_file_exists_validator).takes_value(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")
.value_parser(pathbuf_file_exists_validator).takes_value(true).required(true))
.arg(arg!(-o --"output-dir" <OUTPUTDIR> "output directory where quantification results will be written").value_parser(value_parser!(PathBuf)).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))
.value_parser(pathbuf_file_exists_validator).takes_value(true))
.arg(arg!(-o --"output-dir" <OUTPUTDIR> "output directory where quantification results will be written").value_parser(value_parser!(PathBuf)).takes_value(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).value_parser(pathbuf_file_exists_validator))
.arg(arg!(--"quant-subset" [SFILE] "file containing list of barcodes to quantify, those not in this list will be ignored").value_parser(pathbuf_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 @@ -426,8 +397,14 @@ fn main() -> anyhow::Result<()> {
let input_dir: &PathBuf = t.get_one("input-dir").unwrap();
let output_dir: &PathBuf = t.get_one("output-dir").unwrap();
let tg_map: &PathBuf = t.get_one("tg-map").unwrap();
let resolution: ResolutionStrategy = *t.get_one("resolution").unwrap();
let sa_model: SplicedAmbiguityModel = *t.get_one("sa-model").unwrap();
let resolution = t
.get_one::<ResolutionStrategy>("resolution")
.unwrap()
.clone();
let sa_model = t
.get_one::<SplicedAmbiguityModel>("sa-model")
.unwrap()
.clone();
let small_thresh = *t.get_one("small-thresh").unwrap();
let filter_list: Option<&PathBuf> = t.get_one("quant-subset");
let large_graph_thresh: usize = *t.get_one("large-graph-thresh").unwrap();
Expand Down
2 changes: 1 addition & 1 deletion src/quant.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -101,7 +101,7 @@ impl FromStr for ResolutionStrategy {
"trivial" => Ok(ResolutionStrategy::Trivial),
"cr-like" => Ok(ResolutionStrategy::CellRangerLike),
"cr-like-em" => Ok(ResolutionStrategy::CellRangerLikeEm),
"parsimony-em" | "full" => Ok(ResolutionStrategy::ParsimonyEm),
"parsimony-em" => Ok(ResolutionStrategy::ParsimonyEm),
"parsimony" => Ok(ResolutionStrategy::Parsimony),
"parsimony-gene" => Ok(ResolutionStrategy::ParsimonyGene),
"parsimony-gene-em" => Ok(ResolutionStrategy::ParsimonyGeneEm),
Expand Down

0 comments on commit 23eb300

Please sign in to comment.