getseqs

#!/bin/env bash
helpstr="GETSEQS - Extract sequences from a FASTX file based on a pattern file
Usage getseqs [OPTIONS] SEQ_FILE HEADER_FILE

Positional arguments:
 1: The FASTA or FASTQ sequence file from which to take headers
 2: A file containing a list of patterns (one per line) to match against
    sequence headers
Any sequence in the sequence file whose header matches any pattern in the
pattern file will be included in the output

Options:
 -q: Sequence file is in FASTQ format (default: FASTA)
 -o: Path to output file (default: prints to stdout)
 -h: Print this help message and exit"

unset isfastq outfile seqfile headfile
while [ $OPTIND -le $# ]; do
    # Optional arguments
    while getopts "qo:h" opt; do
        case "$opt" in
            q)
                isfastq="true"
                ;;
            o)
                outfile=$OPTARG
                ;;
            # Else:
            h)
                echo "$helpstr"
                exit
                ;;
            *)
                echo "Invalid argument:" $opt >&2
                echo "$helpstr"
                exit 1
                ;;
        esac
    done

    # Positional arguments:

    if [[ -z "$seqfile" ]]; then
        seqfile=${@:$OPTIND:1}
        OPTIND=$(expr $OPTIND + 1)
    elif [[ -z "$headfile" ]]; then
        headfile=${@:$OPTIND:1}
        OPTIND=$(expr $OPTIND + 1)
    fi
done
shift $((OPTIND-1))

# Errors if positional arguments missing:
if [[ -z "$seqfile" ]]; then
    >&2 echo "Error: Sequence file required."
    exit 1
fi
if [[ -z "$headfile" ]]; then
    >&2 echo "Error: Header list file required."
    exit 1
fi

n=1
if [[ "$isfastq" == "true" ]]; then n=3; fi

if [[ -n "$outfile" ]]; then
    grep -f "$headfile" -A "$n" "$seqfile" --no-group-separator > "$outfile"
else
    grep -f "$headfile" -A "$n" "$seqfile" --no-group-separator
fi
exit