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
macs2-stranded
#!/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"

# help message
help()
{
    echo "usage: $SCRIPTNAME <options> <bam-file>+"
    echo ""
    echo "mandatory arguments:"
    echo "-n NAME name of the experiment; mandatory"
    echo ""
    echo "optional arguments:"
    echo "--keep-temp keep temporary files"
    echo "-g GSIZE approximate size of the genome (for MACS); default = $GSIZE"
    echo "-q 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="$2"; shift 2;;
        -g) GSIZE="$2"; shift 2;;
        -q) QVALUE="$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

BAMS=("$@")


#### Run

echo "Calling peaks"

macs_pos_dir="${NAME}.pos.macs"
macs_neg_dir="${NAME}.neg.macs"


if [[ ${#BAMS[@]} -gt 1 ]]; then
    CAT_CMD="samtools cat -o -"
else
    CAT_CMD="cat"
fi

$CAT_CMD "${BAMS[@]}" | samtools view | head -100 > peek.sam
TAG_SIZE=$(( $(cut -f 10 peek.sam | wc -c) / $(cat peek.sam | wc -l) ))

macs2 callpeak -t <($CAT_CMD "${BAMS[@]}" | samtools view -F 16 -b - |  bedtools bamtobed -i - -split) \
    --outdir "${macs_pos_dir}" -s $TAG_SIZE --nomodel -f BED -g "$GSIZE" \
    -n "${NAME}.pos" -q "$QVALUE" & pos_pid="$!"
macs2 callpeak -t <($CAT_CMD "${BAMS[@]}" | samtools view -f 16 -b - |  bedtools bamtobed -i - -split) \
    --outdir "${macs_neg_dir}" -s $TAG_SIZE --nomodel -f BED -g "$GSIZE" \
    -n "${NAME}.neg" -q "$QVALUE" & neg_pid="$!"

wait $pos_pid 
wait $neg_pid

echo "Combining peaks"
 
cat <(sed "s/\t\.\t/\t+\t/" "${macs_pos_dir}/${NAME}.pos_peaks.narrowPeak") \
    <(sed "s/\t\.\t/\t-\t/" "${macs_neg_dir}/${NAME}.neg_peaks.narrowPeak") \
    > ${NAME}_peaks.narrowPeak

if [ -z "${KEEP_TEMP}" ]; then
    rm -rv "${macs_pos_dir}" "${macs_neg_dir}"
fi

echo "Done"
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