Merge pull request #54 from Roco-scientist/error

Error

Cargo.toml

@@ -1,7 +1,7 @@
 [package]
 name = "barcode-count"
 description = "NGS barcode counter for DEL, CRISPR-seq, and Barcode-seq"
-version = "0.9.3"
+version = "0.9.4"
 edition = "2021"
 license = "Apache-2.0"
 readme = "README.md"
@@ -16,12 +16,12 @@ bench = false
 path = "src/main.rs"
 
 [dependencies]
+anyhow = "1.0"
 rayon = "1.5"
 regex = "1.5"
 clap = "2.33.0"
 itertools = "0.10"
 num_cpus = "1.0"
 flate2 = "1"
 chrono = "0.4"
-custom_error = "1.9"
 num-format = "0.4"

src/arguments.rs

@@ -0,0 +1,216 @@
+use anyhow::{Context, Result};
+use chrono::Local;
+use clap::{crate_version, App, Arg};
+
+/// A struct that contains and initiates all input arguments
+pub struct Args {
+    pub fastq: String,                           // fastq file path
+    pub format: String,                          // format scheme file path
+    pub sample_barcodes_option: Option<String>,  // sample barcode file path.  Optional
+    pub counted_barcodes_option: Option<String>, // building block barcode file path. Optional
+    pub output_dir: String,                      // output directory.  Deafaults to './'
+    pub threads: u8, // Number of threads to use.  Defaults to number of threads on the machine
+    pub prefix: String, // Prefix string for the output files
+    pub merge_output: bool, // Whether or not to create an additional output file that merges all samples
+    pub barcodes_errors_option: Option<u8>, // Optional input of how many errors are allowed in each building block barcode.  Defaults to 20% of the length
+    pub sample_errors_option: Option<u8>, // Optional input of how many errors are allowed in each sample barcode.  Defaults to 20% of the length
+    pub constant_errors_option: Option<u8>, // Optional input of how many errors are allowed in each constant region barcode.  Defaults to 20% of the length
+    pub min_average_quality_score: f32,
+    pub enrich: bool,
+}
+
+impl Args {
+    pub fn new() -> Result<Self> {
+        let total_cpus = num_cpus::get().to_string();
+        let today = Local::today().format("%Y-%m-%d").to_string();
+        // parse arguments
+        let args = App::new("NGS-Barcode-Count")
+        .version(crate_version!())
+        .author("Rory Coffey <coffeyrt@gmail.com>")
+        .about("Counts barcodes located in sequencing data")
+        .arg(
+            Arg::with_name("fastq")
+                .short("f")
+                .long("fastq")
+                .takes_value(true)
+                .required(true)
+                .help("FastQ file"),
+        )
+        .arg(
+            Arg::with_name("format_file")
+                .short("q")
+                .long("sequence-format")
+                .takes_value(true)
+                .required(true)
+                .help("Sequence format file"),
+        )
+        .arg(
+            Arg::with_name("sample_file")
+                .short("s")
+                .long("sample-barcodes")
+                .takes_value(true)
+                .help("Sample barcodes file"),
+        )
+        .arg(
+            Arg::with_name("barcode_file")
+                .short("c")
+                .long("counted-barcodes")
+                .takes_value(true)
+                .help("Counted barcodes file"),
+        )
+        .arg(
+            Arg::with_name("threads")
+                .short("t")
+                .long("threads")
+                .takes_value(true)
+                .default_value(&total_cpus)
+                .help("Number of threads"),
+        )
+        .arg(
+            Arg::with_name("dir")
+                .short("o")
+                .long("output-dir")
+                .takes_value(true)
+                .default_value("./")
+                .help("Directory to output the counts to"),
+        )
+        .arg(
+            Arg::with_name("prefix")
+                .short("p")
+                .long("prefix")
+                .takes_value(true)
+                .default_value(&today)
+                .help("File prefix name.  THe output will end with '_<sample_name>_counts.csv'"),
+        )
+        .arg(
+            Arg::with_name("merge-output")
+                .short("m")
+                .long("merge-output")
+                .takes_value(false)
+                .help("Merge sample output counts into a single file.  Not necessary when there is only one sample"),
+        )
+        .arg(
+            Arg::with_name("enrich")
+                .long("enrich")
+                .short("e")
+                .takes_value(false)
+                .help("Create output files of enrichment for single and double synthons/barcodes"),
+        )
+        .arg(
+            Arg::with_name("max_barcode")
+                .long("max-errors-counted-barcode")
+                .takes_value(true)
+                .help("Maximimum number of sequence errors allowed within each counted barcode. Defaults to 20% of the total."),
+        )
+        .arg(
+            Arg::with_name("max_sample")
+                .long("max-errors-sample")
+                .takes_value(true)
+                .help("Maximimum number of sequence errors allowed within sample barcode. Defaults to 20% of the total."),
+        )
+        .arg(
+            Arg::with_name("max_constant")
+                .long("max-errors-constant")
+                .takes_value(true)
+                .help("Maximimum number of sequence errors allowed within constant region. Defaults to 20% of the total."),
+        )
+        .arg(
+            Arg::with_name("min")
+                .long("min-quality")
+                .takes_value(true)
+                .default_value("0")
+                .help("Minimum average read quality score per barcode"),
+        )
+        .get_matches();
+
+        let sample_barcodes_option;
+        if let Some(sample) = args.value_of("sample_file") {
+            sample_barcodes_option = Some(sample.to_string())
+        } else {
+            sample_barcodes_option = None
+        }
+
+        let counted_barcodes_option;
+        if let Some(barcodes) = args.value_of("barcode_file") {
+            counted_barcodes_option = Some(barcodes.to_string())
+        } else {
+            counted_barcodes_option = None
+        }
+
+        let barcodes_errors_option;
+        if let Some(barcodes) = args.value_of("max_barcode") {
+            barcodes_errors_option = Some(
+                barcodes
+                    .parse::<u8>()
+                    .context("Unable to convert maximum barcode errors to an integer")?,
+            )
+        } else {
+            barcodes_errors_option = None
+        }
+
+        let sample_errors_option;
+        if let Some(sample) = args.value_of("max_sample") {
+            sample_errors_option = Some(
+                sample
+                    .parse::<u8>()
+                    .context("Unable to convert maximum sample errors to an integer")?,
+            )
+        } else {
+            sample_errors_option = None
+        }
+
+        let constant_errors_option;
+        if let Some(constant) = args.value_of("max_constant") {
+            constant_errors_option = Some(
+                constant
+                    .parse::<u8>()
+                    .context("Unable to convert maximum constant errors to an integer")?,
+            )
+        } else {
+            constant_errors_option = None
+        }
+
+        let merge_output;
+        if args.is_present("merge-output") {
+            merge_output = true
+        } else {
+            merge_output = false
+        }
+        let enrich;
+        if args.is_present("enrich") {
+            enrich = true
+        } else {
+            enrich = false
+        }
+        let fastq = args.value_of("fastq").unwrap().to_string();
+        let format = args.value_of("format_file").unwrap().to_string();
+        let output_dir = args.value_of("dir").unwrap().to_string();
+        let threads = args
+            .value_of("threads")
+            .unwrap()
+            .parse::<u8>()
+            .context("Unable to convert threads to an integer")?;
+        let prefix = args.value_of("prefix").unwrap().to_string();
+        let min_average_quality_score = args
+            .value_of("min")
+            .unwrap()
+            .parse::<f32>()
+            .context("Unable to convert min score to a float")?;
+
+        Ok(Args {
+            fastq,
+            format,
+            sample_barcodes_option,
+            counted_barcodes_option,
+            output_dir,
+            threads,
+            prefix,
+            merge_output,
+            barcodes_errors_option,
+            sample_errors_option,
+            constant_errors_option,
+            min_average_quality_score,
+            enrich,
+        })
+    }
+}