Fasta assembly metrics by assem_mets

assem_mets.sh

##/usr/bin/env bash

# ------------------------------------------------------------------------------
# Script: Assembly metrics
# Author: Anuj Sharma
# Github: rknx/
# Email: rknx@outlook.com
# Description: This script is used to calculate various assembly metrics from
#   a single multiFASTA file, often a genome assembly.
# Last modified: <2022/08/04>
# Copyright (C) 2022 Anuj Sharma (rknx@outlook.com)
# Permission to copy and modify is granted under the GPL license
# ------------------------------------------------------------------------------

# --- Default values -----------------------------------------------------------

VERSION=0.4.0
XLOG=
XTMP=

# --- Usage --------------------------------------------------------------------

read -r -d '' USAGE << EOF
USAGE
	$(basename "$0") [options] [--] ... [infile]

DESCRIPTION
	This script computes several assembly metrics for a multiFASTA file.

IMPLEMENTATION
	version         $(basename ${0%.sh}) v$VERSION
	author          Anuj Sharma
	copyright       Copyright © 2022 Anuj Sharma (rknx@outlook.com)
	license         GNU General Public License

OPTIONS
    -h | --help
        Display help text.
    -v | --version
        Display software version.
    -o | --outfile []
        Specify output file.
    -s | --short
        Do not display individual contig information.
    -V | --verbose
        Write debug messages to logfile.
EOF

# --- Options processing -------------------------------------------------------

# Return help if there are no arguments
if [ $# == 0 ] ; then echo "$USAGE"; exit 1; fi

# Pre-process arguments
ARGS=()
ENDOPT=
while [[ $# -gt 0 ]]; do
	arg="$1"; shift
	case "${ENDOPT}${arg}" in
		--)    ARGS+=("$arg"); ENDOPT=1 ;;
		--*=*) ARGS+=("${arg%%=*}" "${arg#*=}") ;;
		--*)   ARGS+=("$arg") ;;
		-*)    for i in $(seq 2 ${#arg}); do ARGS+=("-${arg:i-1:1}"); done ;;
		*)     ARGS+=("$arg") ;;
  esac
done

# Apply pre-processed options
set -- "${ARGS[@]}"

# Parse options
ENDOPT=
SHORT=
INFILES=()
while [[ $# -gt 0 ]]; do
  case "${ENDOPT}${1}" in
	# -x|--xxxxx) fun ;;                     # option
	# -x|--xxxxx) shift; var="$1" ;;         # one time argument with value
	# -x|--xxxxx) shift; multivar+=("$1") ;; # repeated argument with values
    -h|--help)           echo "$USAGE" >&2; exit 0 ;;
    -v|--version)        echo "$(basename ${0%.sh}) v$VERSION" >&2; exit 0 ;;
    -V|--verbose)        export XLOG=1 ;;
    -o|--outfile)        shift; export OUTFILE="$1" ;;
    -s|--short)          export SHORT=1;;
	--)                  ENDOPT=1 ;;
    -*)                  echo "ERROR: Unrecognized argument: $1" >&2;
                         echo "$USAGE" >&2; exit 1 ;;
    *)                   INFILE+=("$1") ;;
  esac
  shift
done

# Helper function for logging and outfile
source "$(dirname $(which "$0"))/logging.sh"

# Check if input is provided
[[ -z "$INFILE" ]] && \
    __ts "No input FASTA file for computing metrics." && \
    exit 1

# Check if multiple input is provided
[[ "${#INFILE[@]}" -gt "1" ]] && \
    __ts "Multiple input files provided. Only first one is used." && \
    INFILE=${INFILE[0]}

# Input information

__tsv "Processing file: $INFILE."

echo "Input file: $INFILE"

# Get lengths of contigs

__tsv "Calculating contig lengths."

arr=( $(
    awk '
        BEGIN{RS=">";ORS="\n";FS="\n"}
        NR>1{$1 = ""; print gsub(/[aAtTuUwWgGcCsSrRyYkKmMbBdDhHvVnN]/, "")}
    ' "$INFILE" | \
        sort -nr
) )

__tsv "Finished contig length."

# Get length of assembly

size=$((${arr[@]/%/+}0))

# Basic assembly information

__tsv "Calculating general assembly information."

echo -e "\n---- Assembly overview -------------------------"

echo "Total assembly length: $size"
echo "Number of contigs:     ${#arr[@]}"
echo "Largest contig size:   ${arr[0]}"
echo "Smallest contig size:  ${arr[-1]}"

__tsv "Calculating GC percent."

grep -v ">" "$INFILE" | tr -d '\n' | \
    awk '{
        gcs = gsub(/[gGcCsS]/, "")
        atuw = gsub(/[aAtTuUwW]/, "")
        printf "GC content: %.2f%%\n", gcs * 100 / ( gcs + atuw )
    }'

__tsv "Finished general assembly information."

# Assembly quality (N50 etc.)

__tsv "Calculating assembly quality information."

echo -e "\n---- Assembly quality --------------------------"

for i in 50 75 90
do

    __tsv "Processing N$i."

    awk -v t="$size" -vRS=" " -vf="$i" '{d++}(c+=$1)>=t*f/100 \
        {printf "N%s: %s\tL%s: %s\n", f, $1, f, d; exit}' <<< ${arr[@]}
done

__tsv "Finished assembly quality information."

# End if short output

[[ "$SHORT" -eq 1 ]] && \
    __tsv "Short output complete." && \
    exit 1

# Contig size distribution

__tsv "Calculating contig size distribution."

echo -e "\n---- Contig size distribution ------------------"

for i in {3..6}
do
    awk -vRS=" " -vf=$(( 10**$i )) '
        $1 < f { printf ">%-10s\t%s contigs\t%s bp\n", f, d+0, c+0; exit }
        { d++; c+=$1 }
    ' <<< ${arr[@]}
done

__tsv "Finished contig size distribition."

# Individual contig information

__tsv "Calculating contig specific values."

echo -e "\n---- Contig information ------------------------"

awk -vRS=">" -vORS="\n" -vFS="\n" '
    BEGIN {print "Name", "Length", "%GC"}
    NR>1 {
        split($1, j, " "); $1 = ""
        atuw=gsub(/[aAtTuUwW]/, "")
        gcs=gsub(/[gGcCsS]/, "")
        rykmbdhvn=gsub(/[rRyYkKmMbBdDhHvVnN]/, "")
        printf "%s %d %.2f\n", j[1], atuw+gcs+rykmbdhvn, gcs/(gcs+atuw)*100
    }
' "$INFILE" | column -t

__tsv "Finished contig specific values."

__tsv "Assembly metric all done for $INFILE."

Error on N50 calculation in v0.3.0 is fixed in v0.4.0