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|
--
-- This is file `pgfmolbio.chromatogram.lua',
-- generated with the docstrip utility.
--
-- The original source files were:
--
-- pgfmolbio.dtx (with options: `pmb-chr-lua')
--
-- Copyright (C) 2011 by Wolfgang Skala
--
-- This work may be distributed and/or modified under the
-- conditions of the LaTeX Project Public License, either version 1.3
-- of this license or (at your option) any later version.
-- The latest version of this license is in
-- http://www.latex-project.org/lppl.txt
-- and version 1.3 or later is part of all distributions of LaTeX
-- version 2005/12/01 or later.
--
module("pgfmolbio.chromatogram", package.seeall)
local ALL_BASES = {"A", "C", "G", "T"}
local PGFKEYS_PATH = "/pgfmolbio/chromatogram/"
local header, samples,
peaks, parms,
selectedPeaks,
lastScfFile
local function baseToSampleIndex (baseIndex)
local result = tonumber(baseIndex)
if result then
return result
else
result = string.match(baseIndex, "base%s*(%d+)")
if tonumber(result) then
return peaks[tonumber(result)].offset
end
end
end
local function stdProbStyle (prob)
local color = ""
if prob >= 0 and prob < 10 then
color = "black"
elseif prob >= 10 and prob < 20 then
color = "pmbTraceRed"
elseif prob >= 20 and prob < 30 then
color = "pmbTraceYellow"
else
color = "pmbTraceGreen"
end
return "ultra thick, " .. color
end
local function findBasesInStr (target)
if not target then return end
local result = {}
for _, v in ipairs(ALL_BASES) do
if string.find(string.upper(target), v) then
table.insert(result, v)
end
end
return result
end
function getMinMaxProbability ()
local minProb = 0
local maxProb = 0
for _, currPeak in ipairs(selectedPeaks) do
for __, currProb in pairs(currPeak.prob) do
if currProb > maxProb then maxProb = currProb end
if currProb < minProb then minProb = currProb end
end
end
return minProb, maxProb
end
local function getRange (rangeInput, regExp)
local lower, upper = string.match(rangeInput, regExp)
local step = string.match(rangeInput, "step%s*(%d*)")
return lower, upper, step
end
local function readInt (file, n, offset)
if offset then file:seek("set", offset) end
local result = 0
for i = 1, n do
result = result * 0x100 + string.byte(file:read(1))
end
return result
end
local function evaluateScfFile (file)
samples = {A = {}, C = {}, G = {}, T = {}}
peaks = {}
header = {
magicNumber = readInt(file, 4, 0),
samplesNumber = readInt(file, 4),
samplesOffset = readInt(file, 4),
basesNumber = readInt(file, 4),
leftClip = readInt(file, 4),
rightClip = readInt(file, 4),
basesOffset = readInt(file, 4),
comments = readInt(file, 4),
commentsOffset = readInt(file, 4),
version = readInt(file, 4),
sampleSize = readInt(file, 4),
codeSet = readInt(file, 4),
privateSize = readInt(file, 4),
privateOffset = readInt(file, 4)
}
if header.magicNumber ~= 0x2E736366 then
tex.error("Magic number in scf file '" .. lastScfFile .. "' corrupt!")
end
if header.version ~= 0x332E3030 then
tex.error("Scf file '" .. lastScfFile .. "' is not version 3.00!")
end
file:seek("set", header.samplesOffset)
for baseIndex, baseName in ipairs(ALL_BASES) do
for i = 1, header.samplesNumber do
samples[baseName][i] = readInt(file, header.sampleSize)
end
for _ = 1, 2 do
local preValue = 0
for i = 1, header.samplesNumber do
samples[baseName][i] = samples[baseName][i] + preValue
if samples[baseName][i] > 0xFFFF then
samples[baseName][i] = samples[baseName][i] - 0x10000
end
preValue = samples[baseName][i]
end
end
end
for i = 1, header.basesNumber do
peaks[i] = {
offset = readInt(file, 4),
prob = {A, C, G, T},
base
}
end
for i = 1, header.basesNumber do
peaks[i].prob.A = readInt(file, 1)
end
for i = 1, header.basesNumber do
peaks[i].prob.C = readInt(file, 1)
end
for i = 1, header.basesNumber do
peaks[i].prob.G = readInt(file, 1)
end
for i = 1, header.basesNumber do
peaks[i].prob.T = readInt(file, 1)
end
for i = 1, header.basesNumber do
peaks[i].base = string.char(readInt(file, 1))
end
end
function readScfFile (filename)
if filename ~= lastScfFile then
lastScfFile = filename
local scfFile, errorMsg = io.open(filename, "rb")
if not scfFile then tex.error(errorMsg) end
evaluateScfFile(scfFile)
scfFile:close()
end
end
function setParameters (newParms)
local sampleRangeMin, sampleRangeMax, sampleRangeStep =
getRange(
newParms.sampleRange or "1 to 500 step 1",
"([base]*%s*%d+)%s*to%s*([base]*%s*%d+)"
)
local baseNumberRangeMin, baseNumberRangeMax, baseNumberRangeStep =
getRange(
newParms.baseNumberRange or "auto to auto step 10",
"([auto%d]*)%s+to%s+([auto%d]*)"
)
parms = {
sampleMin = baseToSampleIndex(sampleRangeMin) or 1,
sampleMax = baseToSampleIndex(sampleRangeMax) or 500,
sampleStep = sampleRangeStep or 1,
xUnit = newParms.xUnit or dimen("0.2mm")[1],
yUnit = newParms.yUnit or dimen("0.01mm")[1],
samplesPerLine = newParms.samplesPerLine or 500,
baselineSkip = newParms.baselineSkip or dimen("3cm")[1],
canvasHeight= newParms.canvasHeight or dimen("2cm")[1],
traceStyle = {
A = PGFKEYS_PATH .. "trace A style@style",
C = PGFKEYS_PATH .. "trace C style@style",
G = PGFKEYS_PATH .. "trace G style@style",
T = PGFKEYS_PATH .. "trace T style@style"
},
tickStyle = {
A = PGFKEYS_PATH .. "tick A style@style",
C = PGFKEYS_PATH .. "tick C style@style",
G = PGFKEYS_PATH .. "tick G style@style",
T = PGFKEYS_PATH .. "tick T style@style"
},
tickLength = newParms.tickLength or dimen("1mm")[1],
baseLabelText = {
A = "\\csname pmb@chr@base label A text\\endcsname",
C = "\\csname pmb@chr@base label C text\\endcsname",
G = "\\csname pmb@chr@base label G text\\endcsname",
T = "\\csname pmb@chr@base label T text\\endcsname"
},
baseLabelStyle = {
A = PGFKEYS_PATH .. "base label A style@style",
C = PGFKEYS_PATH .. "base label C style@style",
G = PGFKEYS_PATH .. "base label G style@style",
T = PGFKEYS_PATH .. "base label T style@style"
},
showBaseNumbers = newParms.showBaseNumbers,
baseNumberMin = tonumber(baseNumberRangeMin) or -1,
baseNumberMax = tonumber(baseNumberRangeMax) or -1,
baseNumberStep = tonumber(baseNumberRangeStep) or 10,
probDistance = newParms.probDistance or dimen("0.8cm")[1],
probStyle = newParms.probStyle or stdProbStyle,
tracesDrawn = findBasesInStr(newParms.tracesDrawn) or ALL_BASES,
ticksDrawn = newParms.ticksDrawn or "ACGT",
baseLabelsDrawn = newParms.baseLabelsDrawn or "ACGT",
probabilitiesDrawn = newParms.probabilitiesDrawn or "ACGT",
coordUnit = "mm",
coordFmtStr = "%s%s"
}
end
function printTikzChromatogram ()
selectedPeaks = {}
local tIndex = 1
for rPeakIndex, currPeak in ipairs(peaks) do
if currPeak.offset >= parms.sampleMin
and currPeak.offset <= parms.sampleMax then
selectedPeaks[tIndex] = {
offset = currPeak.offset + 1 - parms.sampleMin,
base = currPeak.base,
prob = currPeak.prob,
baseIndex = rPeakIndex,
probXRight = parms.sampleMax + 1 - parms.sampleMin
}
if tIndex > 1 then
selectedPeaks[tIndex-1].probXRight =
(selectedPeaks[tIndex-1].offset
+ selectedPeaks[tIndex].offset) / 2
end
tIndex = tIndex + 1
end
end
if tIndex > 1 then
if parms.baseNumberMin == -1 then
parms.baseNumberMin = selectedPeaks[1].baseIndex
end
if parms.baseNumberMax == -1 then
parms.baseNumberMax = selectedPeaks[tIndex-1].baseIndex
end
end
local samplesLeft = parms.sampleMax - parms.sampleMin + 1
local currLine = 0
while samplesLeft > 0 do
local yLower = -currLine * parms.baselineSkip
local yUpper = -currLine * parms.baselineSkip + parms.canvasHeight
local xRight =
(math.min(parms.samplesPerLine, samplesLeft) - 1) * parms.xUnit
tex.sprint(
"\\draw[" .. PGFKEYS_PATH .. "canvas style@style] (" ..
number.todimen(0, parms.coordUnit, parms.coordFmtStr) ..
", " ..
number.todimen(yLower, parms.coordUnit, parms.coordFmtStr) ..
") rectangle (" ..
number.todimen(xRight, parms.coordUnit, parms.coordFmtStr) ..
", " ..
number.todimen(yUpper, parms.coordUnit, parms.coordFmtStr) ..
");\n"
)
samplesLeft = samplesLeft - parms.samplesPerLine
currLine = currLine + 1
end
for _, baseName in ipairs(parms.tracesDrawn) do
tex.sprint("\\draw[" .. parms.traceStyle[baseName] .. "] ")
local currSampleIndex = parms.sampleMin
local sampleX = 1
local x = 0
local y = 0
local currLine = 0
local firstPointInLine = true
while currSampleIndex <= parms.sampleMax do
x = ((sampleX - 1) % parms.samplesPerLine) * parms.xUnit
y = samples[baseName][currSampleIndex] * parms.yUnit
- currLine * parms.baselineSkip
if sampleX % parms.sampleStep == 0 then
if not firstPointInLine then
tex.sprint(" -- ")
else
firstPointInLine = false
end
tex.sprint(
"(" ..
number.todimen(x, parms.coordUnit, parms.coordFmtStr) ..
", " ..
number.todimen(y, parms.coordUnit, parms.coordFmtStr) ..
")"
)
end
if sampleX ~= parms.sampleMax + 1 - parms.sampleMin then
if sampleX >= (currLine + 1) * parms.samplesPerLine then
currLine = currLine + 1
tex.sprint(";\n\\draw[" .. parms.traceStyle[baseName] .. "] ")
firstPointInLine = true
end
else
tex.sprint(";\n")
end
sampleX = sampleX + 1
currSampleIndex = currSampleIndex + 1
end
end
local currLine = 0
local lastProbX = 1
local probRemainder = false
for _, currPeak in ipairs(selectedPeaks) do
while currPeak.offset > (currLine + 1) * parms.samplesPerLine do
currLine = currLine + 1
end
local x = ((currPeak.offset - 1) % parms.samplesPerLine) * parms.xUnit
local yUpper = -currLine * parms.baselineSkip
local yLower = -currLine * parms.baselineSkip - parms.tickLength
local tickOperation = ""
if string.find(string.upper(parms.ticksDrawn), currPeak.base) then
tickOperation = "--"
end
tex.sprint(
"\\draw[" ..
parms.tickStyle[currPeak.base] ..
"] (" ..
number.todimen(x, parms.coordUnit, parms.coordFmtStr) ..
", " ..
number.todimen(yUpper, parms.coordUnit, parms.coordFmtStr) ..
") " ..
tickOperation ..
" (" ..
number.todimen(x, parms.coordUnit, parms.coordFmtStr) ..
", " ..
number.todimen(yLower, parms.coordUnit, parms.coordFmtStr) ..
")"
)
if string.find(string.upper(parms.baseLabelsDrawn), currPeak.base) then
tex.sprint(
" node[" ..
parms.baseLabelStyle[currPeak.base] ..
"] {" ..
parms.baseLabelText[currPeak.base] ..
"}"
)
end
if parms.showBaseNumbers
and currPeak.baseIndex >= parms.baseNumberMin
and currPeak.baseIndex <= parms.baseNumberMax
and (currPeak.baseIndex - parms.baseNumberMin)
% parms.baseNumberStep == 0 then
tex.sprint(
" node[" .. PGFKEYS_PATH .. "base number style@style] {\\strut " ..
currPeak.baseIndex ..
"}"
)
end
tex.sprint(";\n")
if probRemainder then
tex.sprint(probRemainder)
probRemainder = false
end
local drawCurrProb = string.find(
string.upper(parms.probabilitiesDrawn),
currPeak.base
)
local xLeft = lastProbX - 1 - currLine * parms.samplesPerLine
if xLeft < 0 then
local xLeftPrev = (parms.samplesPerLine + xLeft) * parms.xUnit
local xRightPrev = (parms.samplesPerLine - 1) * parms.xUnit
local yPrev = -(currLine-1) * parms.baselineSkip - parms.probDistance
if drawCurrProb then
tex.sprint(
"\\draw[" ..
parms.probStyle(currPeak.prob[currPeak.base]) ..
" ] (" ..
number.todimen(xLeftPrev, parms.coordUnit, parms.coordFmtStr) ..
", " ..
number.todimen(yPrev, parms.coordUnit, parms.coordFmtStr) ..
") -- (" ..
number.todimen(xRightPrev, parms.coordUnit, parms.coordFmtStr) ..
", " ..
number.todimen(yPrev, parms.coordUnit, parms.coordFmtStr) ..
");\n"
)
end
xLeft = 0
else
xLeft = xLeft * parms.xUnit
end
local xRight = currPeak.probXRight - 1 - currLine * parms.samplesPerLine
if xRight >= parms.samplesPerLine then
if drawCurrProb then
local xRightNext = (xRight - parms.samplesPerLine) * parms.xUnit
local yNext = -(currLine+1) * parms.baselineSkip - parms.probDistance
probRemainder =
"\\draw[" ..
parms.probStyle(currPeak.prob[currPeak.base]) ..
" ] (" ..
number.todimen(0, parms.coordUnit, parms.coordFmtStr) ..
", " ..
number.todimen(yNext, parms.coordUnit, parms.coordFmtStr) ..
") -- (" ..
number.todimen(xRightNext, parms.coordUnit, parms.coordFmtStr) ..
", " ..
number.todimen(yNext, parms.coordUnit, parms.coordFmtStr) ..
");\n"
end
xRight = (parms.samplesPerLine - 1) * parms.xUnit
else
xRight = xRight * parms.xUnit
end
local y = -currLine * parms.baselineSkip - parms.probDistance
if drawCurrProb then
tex.sprint(
"\\draw[" ..
parms.probStyle(currPeak.prob[currPeak.base]) ..
" ] (" ..
number.todimen(xLeft, parms.coordUnit, parms.coordFmtStr) ..
", " ..
number.todimen(y, parms.coordUnit, parms.coordFmtStr) ..
") -- (" ..
number.todimen(xRight, parms.coordUnit, parms.coordFmtStr) ..
", " ..
number.todimen(y, parms.coordUnit, parms.coordFmtStr) ..
");\n"
)
end
lastProbX = currPeak.probXRight
end
end
--
-- End of file `pgfmolbio.chromatogram.lua'.
|