barcode trimming; fastq conversion

seq/fq2cofq.lua

@@ -0,0 +1,131 @@
+#!/usr/bin/env luajit
+
+function os.getopt(args, ostr)
+	local arg, place = nil, 0;
+	return function ()
+		if place == 0 then -- update scanning pointer
+			if #args == 0 or args[1]:sub(1, 1) ~= '-' then return nil end
+			if #args[1] >= 2 then
+				if args[1]:sub(2, 2) == '-' then -- found "--"
+					table.remove(args, 1);
+					return nil;
+				end
+			end
+			place = 2
+		end
+		local optopt = args[1]:sub(place, place);
+		place = place + 1;
+		local oli = ostr:find(optopt);
+		if optopt == ':' or oli == nil then -- unknown option
+			if optopt == '-' then return nil end
+			if place > #args[1] then
+				table.remove(args, 1);
+				place = 0;
+			end
+			return '?';
+		end
+		oli = oli + 1;
+		if ostr:sub(oli, oli) ~= ':' then -- do not need argument
+			arg = nil;
+			if place > #args[1] then
+				table.remove(args, 1);
+				place = 0;
+			end
+		else -- need an argument
+			if place <= #args[1] then  -- no white space
+				arg = args[1]:sub(place);
+			else
+				table.remove(args, 1);
+				if #args == 0 then -- an option requiring argument is the last one
+					place = 0;
+					if ostr:sub(1, 1) == ':' then return ':' end
+					return '?';
+				else arg = args[1] end
+			end
+			table.remove(args, 1);
+			place = 0;
+		end
+		return optopt, arg;
+	end
+end
+
+function string:split(sep, n)
+	local a, start = {}, 1;
+	sep = sep or "%s+";
+	repeat
+		local b, e = self:find(sep, start);
+		if b == nil then
+			table.insert(a, self:sub(start));
+			break
+		end
+		a[#a+1] = self:sub(start, b - 1);
+		start = e + 1;
+		if n and #a == n then
+			table.insert(a, self:sub(start));
+			break
+		end
+	until start > #self;
+	return a;
+end
+
+function io.xopen(fn, mode)
+	mode = mode or 'r';
+	if fn == nil then return io.stdin;
+	elseif fn == '-' then return (mode == 'r' and io.stdin) or io.stdout;
+	elseif fn:sub(-3) == '.gz' then return (mode == 'r' and io.popen('gzip -dc ' .. fn, 'r')) or io.popen('gzip > ' .. fn, 'w');
+	elseif fn:sub(-4) == '.bz2' then return (mode == 'r' and io.popen('bzip2 -dc ' .. fn, 'r')) or io.popen('bgzip2 > ' .. fn, 'w');
+	else return io.open(fn, mode) end
+end
+
+if #arg < 1 then
+	print('Usage: fq2cgfq.lua [-IF] [-b barcode] <in1.fq> [in2.fq]')
+	os.exit(1)
+end
+
+local is_il13, is_flt, acgtn, bc_len, bc_hash = false, true, {'A', 'C', 'G', 'T', 'N'}, 0
+for o, a in os.getopt(arg, 'IFb:') do
+	if o == 'I' then is_il13 = true
+	elseif o == 'b' then
+		local t = a:split(',')
+		bc_len, bc_hash = #t[1], {}
+		for _, v in ipairs(t) do
+			assert(#v == bc_len)
+			for i = 1, bc_len do
+				for _, j in ipairs(acgtn) do
+					w = v:sub(1, i - 1) .. j .. v:sub(i + 1)
+					bc_hash[w] = true
+				end
+			end
+		end
+	elseif o == 'F' then is_flt = true
+	end
+end
+
+local fp = {io.xopen(arg[1]), nil}
+if arg[2] then fp[2] = io.xopen(arg[2]) end
+while true do
+	local l = {{}, {}}
+	for i = 1, 4 do l[1][i] = fp[1]:read() end
+	if fp[2] then
+		for i = 1, 4 do l[2][i] = fp[2]:read() end
+	end
+	if l[1][4] == nil or (fp[2] and l[2][4] == nil) then break end
+	local bc = bc_len ~= 0 and l[1][2]:sub(1, bc_len) or nil
+	if (is_flt == false or l[1][1]:find('^%S+:%d+:%d+:%d+:%d+:0#0') == nil) and (bc == nil or bc_hash[bc]) then
+		if is_il13 then
+			local q = {{}, {}}
+			for i = 1, #l[1][4] do q[1][i] = string.char(l[1][4]:byte(i) - 31) end
+			l[1][4] = table.concat(q[1])
+			if fp[2] then
+				for i = 1, #l[2][4] do q[2][i] = string.char(l[2][4]:byte(i) - 31) end
+				l[2][4] = table.concat(q[2])
+			end
+		end
+		print(l[1][1], bc) print(l[1][2]:sub(bc_len+1)) print('+') print(l[1][4]:sub(bc_len+1))
+		if fp[2] then
+			print(l[2][1]) print(l[2][2]) print('+') print(l[2][4])
+		end
+	end
+end
+fp[1]:close()
+if fp[2] then fp[2]:close() end