#!/usr/bin/env sh


# For random5k data
function mkarray(){

local indir=$1
local prefix=$2
local outdir=$3
    for i in ${indir}/*.pair
    do 
        basename=${i##*/}
        tmparray=tmp/${basename%.*}.array
        touch ${tmparray}
        # name
        echo ${basename%.*} > ${tmparray}
        eval "cut -f1,4 ${indir}/CNCI_ve.pair > tmp/a"
        eval "../../base/annot_from_file.py -n1 -n2 -v 1 ${indir}/CNCI_ve.pair ${i} |cut -f5 | awk '{if(NR!=1)print}' >> ${tmparray}"
    done

    # Filter out line with empty elements.
    eval "paste tmp/* | ./filter_line.py > ${outdir}/${prefix}.array"
    rm tmp/*
}

# For smallRNE data
function mkarray1(){

local indir=$1
local prefix=$2
local outdir=$3
    for i in ${indir}/*.coding
    do 
        basename=${i##*/}
        tmparray=tmp/${basename%.*}.coding
        touch ${tmparray}
        # name
        echo ${basename%.*} > ${tmparray}
        eval "cut -f1,4 ${indir}/CNCI_ve.coding > tmp/a"
        eval "../../base/annot_from_file.py -n1 -n2 -v 1 ${indir}/CNCI_ve.coding ${i} |cut -f5 | awk '{if(NR!=1)print}' >> ${tmparray}"
    done

    eval "paste tmp/* | ./filter_line.py > ${outdir}/${prefix}.array"
    rm tmp/*
}

function mkarray3()
{
Methods=(CNCI_pl CNCI_ve come1 come2 cpat_fly cpat_human cpat_mouse cpat_zebrafish cpc cpc2 feelnc_ab_cl feelnc_ab_sf feelnc_all_cl feelnc_all_sf feelnc_ff_cl feelnc_ff_sf feelnc_hm_cl feelnc_hm_sf feelnc_ms_cl feelnc_ms_sf feelnc_wm_cl feelnc_wm_sf feelnc_zf_cl feelnc_zf_sf hmmscan1 hmmscan2 hmmscan3 iSeeRNA lncRScan lncScore longdist_GRCh37 longdist_GRCh37_GRCm38 longdist_GRCh38 longdist_GRCh38_GRCm38 longdist_GRCm38 longdist_GRCm38_GRCz10 PLEK plncpro1 plncpro2 rnaplonc1 rnaplonc2)
}

# Golden_human, golden_mouse and mitrans
mkdir tmp
prefix=Mitranscriptome
prefix=golden_human
prefix=golden_mouse
inroot="../../../data/codingf/random5k"
infiles=("pair_mitrans" "pair_human" "pair_mouse")
prefixs=("mitrans" "golden_human" "golden_mouse")
outdir="../../../data/arrays"
for i in ${!prefixs[@]}
do
    mkarray ${inroot}/${infiles[$i]} ${prefixs[$i]} ${outdir}
done

# smallRNE
inroot="../../../data/codingf/smallRNE"
infiles=("all_spe" "simple/merged")
prefixs=("smallRNE_all" "smallRNE_core")
outdir="../../../data/arrays"
for i in ${!prefixs[@]}
do
    mkarray1 ${inroot}/${infiles[$i]} ${prefixs[$i]} ${outdir}
done

# Real data
mkarray1 ../../../data/codingf/realdata/rainbow rainbow ../../../data/arrays
mkarray1 ../../../data/codingf/realdata/seahorse seahorse ../../../data/arrays
rm -d tmp