hitime-docker.sh

#!/bin/bash
set -e

program_name="hitime-docker.sh"
input_filepath=""
output_filepath=""
remaining_args=""

# Help message for using the program.
function show_help {
cat << UsageMessage

${program_name}: detect twin ion signals in Mass Spectrometry data 

Usage:
    ${program_name} [-v] [-h] -i input.mzML -o output.mzML -- -r <RT FWHM scans> -d <M/Z delta> -m <M/Z FWHM ppm> [optional arguments]
    ${program_name} [-v] [-h] -i input.mzML -o output.mzML -- -r <RT FWHM scans> -l <M/Z lower bound> -u <M/Z upper bound>

This is a wrapper for the HiTIME-CPP docker container.

The default use re-scales the peaks in the input file based on their similarity to an ideal twin ion peak.

Using the upper and lower m/z bound options filters for the local maximum and outputs to the specified <outfile>.mzML file, and a text file <outfile>.csv

Example usage:

   ./hitime-docker.sh -i data/testing.mzML -o data/scored.mzML -- -r 10 -d 6.0201 -m 230 -j 2
   ./hitime-docker.sh -i data/scored.mzML -o data/max.scored.mzML -- -r 10 -l 0.3 -u 0.7

UsageMessage

echo "The full set of HiTIME command line arguments are listed below:"
echo

    exec docker run --rm bjpop/hitime --help
}

# echo an error message $1 and exit with status $2
function exit_with_error {
    printf "${program_name}: ERROR: $1\n"
    exit $2
}

absolute_filepath () {
  case "$1" in
    /*) echo "$1";;
    *) echo "$PWD/$1";;
  esac
}

show_version () {
    exec docker run --rm bjpop/hitime --version
}

# Parse the command line arguments and set the global variables language and new_project_name
function parse_args {

    if [ "$#" -lt 1 ]; then
        show_help
        exit 2 
    fi

    local OPTIND opt

    while getopts "hvi:o:" opt; do
        case "${opt}" in
            h)
                show_help
                exit 0
                ;;
            v)
                show_version
                exit 0
                ;;
            i)  input_filepath="${OPTARG}"
                ;;
            o)  output_filepath="${OPTARG}"
                ;;
        esac
    done

    shift $((OPTIND-1))

    [ "$1" = "--" ] && shift

    remaining_args=$@

    if [[ -z ${input_filepath} ]]; then
        exit_with_error "input file not specified: -i <filename>, use -h for help" 2
    fi

    if [[ -z ${output_filepath} ]]; then
        exit_with_error "output file not specified: -o <filename>, use -h for help" 2
    fi

}

parse_args $@

input_dir=$( absolute_filepath $( dirname "${input_filepath}" ))
output_dir=$(absolute_filepath $( dirname "${output_filepath}" ))
input_filename=$( basename "${input_filepath}" )
output_filename=$( basename "${output_filepath}" )

exec docker run --rm -v "${input_dir}:/input/" -v "${output_dir}:/output/" bjpop/hitime -i "/input/${input_filename}" -o "/output/${output_filename}" ${remaining_args}