https://github.com/ctlab/quant3p
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Tip revision: be9977925e9e842cc755f14ced72bbee5c5d6d77 authored by Alexey Sergushichev on 02 December 2019, 17:22 UTC
fixes for htseq & macs2 upgrades
Tip revision: be99779
quant3p
#!/usr/bin/env bash

#### Set up

SCRIPTNAME=`basename $0`
function error() 
{
    local PARENT_LINENO="$1"
    local MESSAGE="$2"
    local CODE="${3:-1}"
    if [[ -n "$MESSAGE" ]] ; then
        echo "$SCRIPTNAME: Error on or near line ${PARENT_LINENO}: ${MESSAGE}; exiting with status ${CODE}"
    else
        echo "$SCRIPTNAME: Error on or near line ${PARENT_LINENO}; exiting with status ${CODE}"
    fi
    exit "${CODE}"
}

trap 'error ${LINENO}' ERR
# setting exit on error and inheriting of ERR trap
set -eE

die()
{
    if [ -n "$@" ]; then
        echo "$@" >&2
    else
        echo "FAILED" >&2
    fi
    exit 1
}


#### Arguments

GSIZE="3e9"
QVALUE="0.01"
NPROC="2"
KEEP_TEMP=""

# help message
help()
{
    echo "usage: $SCRIPTNAME <options> <bam-file>+"
    echo ""
    echo "mandatory arguments:"
    echo "-n NAME name of the experiment; mandatory"
    echo "-g/--gtf GTF annotaion ; mandatory"
    echo ""
    echo "optional arguments:"
    echo "-p NPROC number of processes to do in parallel; default = $NPROC"
    echo "--keep-temp keep temporary files"
    echo "--genome GSIZE approximate size of the genome (for MACS); default = $GSIZE"
    echo "--qvalue QVALUE q-value cutoff (for MACS); default = $QVALUE"
    echo "-h|--help shows this message and exit"
}


if [ $# -eq 0 ]; then
    help
    exit
fi

while true; do
    case "$1" in
        -n|--name) NAME="$2"; shift 2;;
        -g|--gtf) GTF="$2"; shift 2;;
        --genome) GSIZE="$2"; shift 2;;
        --qvalue) QVALUE="$2"; shift 2;;
        -p) NPROC="$2"; shift 2;;
        --keep-temp) KEEP_TEMP="--keep-temp"; shift 1;;
        -h|--help) help; exit 0;;
        --) shift 1; break;;
        -*) die "unrecognized option: $1";;
        *) break;;
    esac
done

if [ -z "$NAME" ]; then
    die "NAME is not specified (try -h for details)"
fi

if [ -z "$GTF" ]; then
    die "GTF is not specified (try -h for details)"
fi

BAMS=("$@")

if [ "${#BAMS}" == 0 ]; then
    die "no bam files specified (try -h for details)"
fi

#### Run

echo "Calling peaks..."
macs2-stranded $KEEP_TEMP -n "${NAME}" -g "${GSIZE}" -q "${QVALUE}" "${BAMS[@]}" | sed "s/^/  /"
peaks="${NAME}"_peaks.narrowPeak

echo "Extending annotaion..."
fixed_gtf="${NAME}.`basename "${GTF}" .gtf`.fixed.gtf"
gtf-extend -g "${GTF}" -p "${peaks}" -o "${fixed_gtf}" | sed "s/^/  /"


export htseq_dir="${NAME}.htseq"
mkdir -p "${htseq_dir}"

count_bam() {
    BAM="$1"
    TAG=`basename "${BAM}" .bam`
    fix-mm -g "${GTF}" "${BAM}" -o - | \
        samtools view -h - | \
        htseq-count --secondary-alignments score -s yes -t exon - "${fixed_gtf}" > "${htseq_dir}/${TAG}.htseq.out"
}


export -f count_bam
export GTF
export fixed_gtf
export KEEP_TEMP

find "${BAMS[@]}" -print0 | xargs -0 -n 1 -P "${NPROC}" bash -c 'count_bam "$@"' _ 

if [ -z "${KEEP_TEMP}" ]; then
    rm "${fixed_gtf}"
    rm "${peaks}"
fi

tags=()
htseq_outs=()

header=""

fields="1"

i=0

for bam in "${BAMS[@]}"
do
    tag=`basename "${bam}" .bam`
    htseq_out="${htseq_dir}/${tag}.htseq.out"
    tags+=("${tag}")
    htseq_outs+=("${htseq_out}")
    header="${header}\t${tag}"
    i=$(($i+2))
    fields="${fields},${i}"
done

cat <(echo -e "${header}") \
    <(paste "${htseq_outs[@]}" | cut -f "${fields}") \
    > "${NAME}.cnt"

if [ -z "${KEEP_TEMP}" ]; then
    for htseq_out in "${htseq_outs[@]}"
    do
        rm "${htseq_out}"
    done

    rmdir "${htseq_dir}"
fi

echo "Done"
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