preprocessFeatureFiles

#!/bin/bash

directory=$1
output_directory=$2
species=$3
data=$4

# DNase-seq or ChIP-seq (standard BED format) for either species
if [ "$data" -eq "0" ]; then
    for filename in "$directory/"*.gz; do
        new_filename=$output_directory"/"`basename "$filename"`
        echo $new_filename
        gzip -cd $filename | awk -v OFS="\t" '{print $1,$2,$3}' | sort -k1,1 -k2,2n | gzip > $new_filename
    done
elif [ "$species" -eq "0" ]; then
    # Human ChromHMM
    if [ "$data" -eq "1" ]; then
        for filename in "$directory/"*.bed.gz; do
            new_filename=$output_directory"/"`basename "$filename"`
            echo $new_filename
            gzip -cd $filename | awk -v OFS="\t" '{print $1,$2,$3,$4}' | sort -k1,1 -k2,2n | gzip > $new_filename
        done
    # Human CAGE
    elif [ "$data" -eq "2" ]; then
        filename=$(ls "$directory/"*.txt.gz)
        new_filename=$output_directory"/"`basename "$filename"`
        echo $new_filename
        gzip -cd $filename | awk '!/^#/ && !/^0/ {print $0}' | awk '{gsub(":", "\t");gsub(",", "\t");gsub("\\.\\.","\t");print}' | cut -f 1-3,5- | sort -k1,1 -k2,2n | gzip > $new_filename
    # Human RNA-seq
    elif [ "$data" -eq "3" ]; then
        for filename in "$directory/"*.bigWig; do
            new_filename=$output_directory"/"`basename "$filename"`".bed"
            echo $new_filename
            ./bigWigToBedGraph $filename $new_filename
            gzip $new_filename
        done
    fi
elif [ "$species" -eq "1" ]; then
    # Mouse ChromHMM
    if [ "$data" -eq "1" ]; then
        for filename in "$directory/"*.bed.gz; do
            new_filename=$output_directory"/"`basename "$filename"`
            echo $new_filename
            gzip -cd $filename | awk -v OFS="\t" '{print $1,$2,$3,$4}' | sort -k1,1 -k2,2n | gzip > $new_filename
        done
    # Mouse CAGE
    elif [ "$data" -eq "2" ]; then
        filename=$(ls "$directory/"*.txt.gz)
        new_filename=$output_directory"/"`basename "$filename"`
        echo $new_filename
        gzip -cd $filename | awk '!/^#/ && !/^0/ {print $0}' | awk '{gsub("::", "\t");gsub(":","\t");gsub("\\.\\.","\t");gsub(",","\t");gsub(";","\t");print}' | cut -f 2-4,7- | sort -k1,1 -k2,2n | gzip > $new_filename
    # Mouse RNA-seq
    elif [ "$data" -eq "3" ]; then
        for filename in "$directory/"*.bigWig; do
            new_filename=$output_directory"/"`basename "$filename"`".bed"
            echo $new_filename
            ./bigWigToBedGraph $filename $new_filename
            gzip $new_filename
        done
    fi
fi