NONPAREIL

Plot Nonpareil results.

URL: https://nonpareil.readthedocs.io/en/latest/

Example

This wrapper can be used in the following way:

rule test_nonpareil_plot:
    input:
        npo="{sample}.npo",
    output:
        pdf="results/{sample}.pdf",
    threads: 1
    log:
        "logs/{sample}.log",
    params:
        label="Plot",
        col="blue",
        enforce_consistency=True,
        star=95,
        correction_factor=True,
        weights_exp="-1.1,-1.2,-0.9,-1.3,-1",
        skip_model=False,
    wrapper:
        "v2.0.0/bio/nonpareil/plot"

Note that input, output and log file paths can be chosen freely.

When running with

snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.

Software dependencies

• nonpareil=3.4.1

Input/Output

Input:

• NPO file

Output:

• PDF file with plot

Params

• label: Plot title.
• col: Color of the curve.
• enforce_consistency: Fails verbosely on insufficient data, otherwise it warns about the inconsistencies and attempts the estimations.
• star: Objective coverage in percentage (i.e., coverage value considered near-complete).
• correction_factor: Apply overlap-dependent correction factor, otherwise redundancy is assumed to equal coverage.
• weights_exp: Vector of values to be tested as exponent of the weights distribution.
• skip_model: Skip model estimation.

Authors

• Filipe G. Vieira

Code

# __author__ = "Filipe G. Vieira"
# __copyright__ = "Copyright 2023, Filipe G. Vieira"
# __license__ = "MIT"

# This script plots results (NPO file) from NonPareil


# Sink the stderr and stdout to the snakemake log file
# https://stackoverflow.com/a/48173272
log.file <- file(snakemake@log[[1]], open = "wt")
base::sink(log.file)
base::sink(log.file, type = "message")


# Loading libraries (order matters)
base::library(package = "Nonpareil", character.only = TRUE)
base::message("Libraries loaded")


params <- list("label" = ifelse("label" %in% base::names(snakemake@params), snakemake@params[["label"]], NA),
                   "col" = ifelse("col" %in% base::names(snakemake@params), snakemake@params[["col"]], NA),
           "enforce_consistency" = ifelse("enforce_consistency" %in% base::names(snakemake@params), as.logical(snakemake@params[["enforce_consistency"]]), FALSE),
           "star" = ifelse("star" %in% base::names(snakemake@params), snakemake@params[["star"]], 95),
           "correction_factor" = ifelse("correction_factor" %in% base::names(snakemake@params), as.logical(snakemake@params[["correction_factor"]]), FALSE),
           "weights_exp" = NA,
           "skip_model" = ifelse("skip_model" %in% base::names(snakemake@params), as.logical(snakemake@params[["skip_model"]]), FALSE)
          )

# Not sure why, by using "ifelse" only keeps the first element of the vector
if ("weights_exp" %in% base::names(snakemake@params)) {
   params[["weights_exp"]] = as.numeric(unlist(strsplit(snakemake@params[["weights_exp"]], ",")))
   }


base::message("Options provided:")
base::print(params)


pdf(snakemake@output[[1]])
Nonpareil.curve(file = snakemake@input[[1]],
            label = params[["label"]],
            col = params[["col"]],
            enforce.consistency = params[["enforce_consistency"]],
            star = params[["star"]],
            correction.factor = params[["correction_factor"]],
            weights.exp = params[["weights_exp"]],
            skip.model = params[["skip_model"]]
           )


base::message("Nonpareil plot saved")
dev.off()


# Proper syntax to close the connection for the log file
# but could be optional for Snakemake wrapper
base::sink(type = "message")
base::sink()