Gedmatch1

gistfile1.txt

--# Main
-- Gedmatch
displayMode(FULLSCREEN)

function setup()  
    ReadData()
    maxSeries=25
    step=20
    charts={image(WIDTH,HEIGHT),image(WIDTH,HEIGHT)}
    CHR=1
    kit1="F446284"
    CreateChart(kit1,CHR)
end

function draw()
    background(0)
    for i=1,#charts do
        sprite(charts[1],WIDTH/2,HEIGHT/2)
    end
end

function CreateChart(k1,c,k2) --k is kit,c is chromosome number
    --collate data
    c=tostring(c)
    local rows={}
    local d=data[k1]
    title="Matches for "..k1.." on chromosome "..c
    local total={}
    for i=1,#d.matches do
        local dm=d.matches[i]
        if dm.chr==c then
            local kk=dm.kit
            rows[kk]=rows[kk] or {}
            rows[kk].total=(rows[kk].total or 0) + dm.cm
            rows[kk].matches=rows[kk].matches or {}
            table.insert(rows[kk].matches,i)
        end
    end
    local s={}
    for i,r in pairs(rows) do
        table.insert(s,{i,r.total})
    end
    table.sort(s,function(a,b) return a[2]>b[2] end) 
    
    --create chart
    local X1,X2=125,WIDTH-25
    local b=bases[tonumber(c)]
    setContext(charts[1])
    background(219, 217, 221, 255)
    fontSize(24)
    fill(0)
    textMode(LEFT)
    text(title,10,HEIGHT-30)
    fontSize(16)
    numSeries=math.min(maxSeries,#s) 
    seriesY={}
    for i=1,numSeries do
        local ss=s[i][1]
        local m=rows[ss].matches[1]
        local h=HEIGHT-40-i*step
        fill(0)
        text(d.matches[m].kit.." ("..math.floor(d.matches[m].cm)..")",10,h)
        local x1=X1+(X2-X1)*d.matches[m].start/b
        local x2=X1+(X2-X1)*d.matches[m].finish/b
        seriesY[i]={h+step/2,d.matches[m].kit,x1,x2}
        fill(91, 143, 186, 255)
        rect(x1,h+0.15*step,x2-x1,step*0.7)
        stroke(91, 143, 186, 255)
        strokeWidth(1)
        line(X1,h+step/2,X2-X1,h+step/2)
    end
    
    --add 2nd chart overlay if required
    if kit2 then
        fill(255, 0, 0, 255)
        local d2=data[k2]
        for i=1,#seriesY do
            local h=HEIGHT-40-i*step
            local k=seriesY[i][2]
            if k==kit2 then 
                rect(seriesY[i][3],h+0.15*step,seriesY[i][4]-seriesY[i][3],step*0.7)       
            else
                local d2=data[k2]
                for j=1,#d2.matches do
                    local dd2=d2.matches[j]
                    if dd2.chr==c and dd2.kit==k then
                        local x1=X1+(X2-X1)*dd2.start/b
                        local x2=X1+(X2-X1)*dd2.finish/b
                        print(k2,x1,x2)
                        rect(x1,h+0.4*step,x2-x1,step*0.2)
                    end
                end
            end
        end       
    end
    
    
    --draw navigation buttons
    leftChr,rightChr=vec2(WIDTH*0.5,HEIGHT-15),vec2(WIDTH*0.5+40,HEIGHT-15)
    navSize=20
    sprite("Tyrian Remastered:Arrow Left",leftChr.x,leftChr.y,navSize)
    sprite("Tyrian Remastered:Arrow Right",rightChr.x,rightChr.y,navSize)
    setContext()
end

function touched(t)
    if t.state==ENDED then
        if vec2(t.x,t.y):dist(leftChr)<navSize then 
            CHR=CHR-1 
            if CHR==0 then CHR=23 end
        elseif vec2(t.x,t.y):dist(rightChr)<navSize then  
            CHR=CHR+1 
            if CHR>23 then CHR=1 end
        else
            for i=1,#seriesY do
                if math.abs(t.y-seriesY[i][1])<step/2 then 
                    kit2=seriesY[i][2]
                    break
                end
            end
        end
        CreateChart(kit1,CHR,kit2)
    end
end



--# Data

data={}
url="https://www.dropbox.com/s/f9n4u28w37jvof4/GedmatchAllM.csv?dl=1"

bases={249250621,243199373,198022430,191154276,180915260,171115067,159138663,146364022,141213431,
       135534747,135006516,133851895,115169878,107349540,102531392,90354753,81195210,78077248,
        59128983,63025520,48129895,51304566,155270560,59373566}

function DownloadData()
    print("Downloading data...")
    http.request(url,SaveData)
end

function SaveData(data,status)
    if status==200 then print("Status=OK") else print("Status code unknown="..status) end
    saveProjectData("GedmatchAll",data)
end

function ReadData()
    local txt=readProjectData("GedmatchAll")
    local rows=Split(txt,"\n")
    table.remove(rows,1) --remove header row
    --print("Records read: "..#rows)
    --put data into tables
    for i=1,#rows do
        local t=Split(rows[i],",")
        local k=t[1]
        if not data[k] then
            data[k]={}
            data[k].kit=t[1]
            data[k].name=t[2]
            data[k].email=t[3]
            data[k].matches={}
            data[k].kits={}
            data[k].chr={}
        end
        local d=data[k]
        table.insert(d.matches,{kit=t[4],chr=t[7],start=t[8],finish=t[9],cm=t[10]})
        d.kits=d.kits or {}
        if t[4]==nil then break end
        d.kits[t[4]]=#d.matches
        d.chr=d.chr or {}
        d.chr[t[7]]=#d.matches
        --table.insert(d.kits,{t[4]=#d.matches})
        --table.insert(d.chr,{t[7],#d.matches})
    end
    print("Data loaded")
    --TestData("F446284")
    --TestMatches("F446284")
end

function Split(txt,delimiter)
    local tbl={}
    for match in (txt..delimiter):gmatch("(.-)"..delimiter) do
        table.insert(tbl,match)
    end
    return tbl
end

function TestData(n)
    local d=data[n] print(d)
    local txt="Test for record "..n
    txt=txt.."\n".."-----------"
    txt=txt.."\n".."kit = "..d.kit
    txt=txt.."\n".."name = "..d.name
    txt=txt.."\n".."email = "..d.email
    txt=txt.."\n".."Matches ----------"
    print(txt) txt=""
    for i=1, #d.matches do
        txt="Match "..i.."...."
        --txt=txt.."\n".."kit = "..d.kits[i]
        --txt=txt.."\n".."chr = "..d.chr[i]
        txt=txt.."\n".."kit = "..d.matches[i].kit
        txt=txt.."\n".."chr = "..d.matches[i].chr
        txt=txt.."\n".."start = "..d.matches[i].start
        txt=txt.."\n".."end = "..d.matches[i].finish
        txt=txt.."\n".."cM = "..d.matches[i].cm
        print(txt)
    end
end

function TestMatches(k)
    local d=data[k]
    print("Testing matches for "..d.kit.."\n--------------------")
    for i=1,#d.matches do
        print(i,d.matches[i][1])
    end
end