From e7d38247bbf068a3cd3c5679ac7aa0453291e1ad Mon Sep 17 00:00:00 2001
From: carneiro <carneiro@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 11 Feb 2011 18:21:31 +0000
Subject: [PATCH] chunkIntervals.lua creates 1Mb interval chunks out of any
 .intervals file. Useful for methods development pipeline datasets.
 remapAmplicons.lua takes a sam file with reads aligned to amplicon
 references, a reference genome , and an amplicon reference mapping table, and
 rewrites the sam file with mappings to the reference sequence.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5230 348d0f76-0448-11de-a6fe-93d51630548a
---
 lua/chunkIntervals.lua | 21 +++++++++++
 lua/remapAmplicons.lua | 84 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 105 insertions(+)
 create mode 100644 lua/chunkIntervals.lua
 create mode 100644 lua/remapAmplicons.lua

diff --git a/lua/chunkIntervals.lua b/lua/chunkIntervals.lua
new file mode 100644
index 000000000..c8ed48aa2
--- /dev/null
+++ b/lua/chunkIntervals.lua
@@ -0,0 +1,21 @@
+local infile = arg[1] or io.stdin
+local outfile = (arg[2] and io.open(arg[2], "w")) or io.stdout
+
+
+local function cutcommas(x)
+  local n = ""
+  for v in x:gmatch("(%d+)") do
+    n = n .. v
+  end
+  if n == "" then return tonumber(x) else return tonumber(n) end
+end
+
+for l in io.lines(infile) do
+  local chr, startPos, endPos = l:match("(.*):(%d+)%-([%d,]+)")
+  startPos = cutcommas(startPos)
+  endPos = cutcommas(endPos)
+  for i=startPos,endPos,1000000 do
+    if endPos > i+999999 then outfile:write(chr..":"..i.."-"..i+999999 .."\n")
+    else outfile:write(chr..":"..i.."-"..endPos.."\n") end
+  end
+end
\ No newline at end of file
diff --git a/lua/remapAmplicons.lua b/lua/remapAmplicons.lua
new file mode 100644
index 000000000..f70748129
--- /dev/null
+++ b/lua/remapAmplicons.lua
@@ -0,0 +1,84 @@
+local ampFile = arg[1]
+local samFile = arg[2]
+local headerFile = io.open(arg[2]:match("(.*).sam")..".header.sam", "w")
+local bodyFile = io.open(arg[2]:match("(.*).sam")..".body.sam", "w")
+
+chrlength = {}
+chrlength["1"] =249250621
+chrlength["2"] =243199373
+chrlength["3"] =198022430
+chrlength["4"] =191154276
+chrlength["5"] =180915260
+chrlength["6"] =171115067
+chrlength["7"] =159138663
+chrlength["8"] =146364022
+chrlength["9"] =141213431
+chrlength["10"]=135534747
+chrlength["11"]=135006516
+chrlength["12"]=133851895
+chrlength["13"]=115169878
+chrlength["14"]=107349540
+chrlength["15"]=102531392
+chrlength["16"]=90354753
+chrlength["17"]=81195210
+chrlength["18"]=78077248
+chrlength["19"]=59128983
+chrlength["20"]=63025520
+chrlength["21"]=48129895
+chrlength["22"]=51304566
+chrlength["X"] =155270560
+chrlength["Y"] =59373566
+chrlength["MT"]=16569
+
+local header = {}
+local reads = {}
+
+-- reads the amplicon file (global var) and returns an amplicon hash table indexed by amplicon name
+local function readAmpliconFile()
+  local amplicons = {}
+  for l in io.lines(ampFile) do
+    local chr, startPos, endPos, ampName = l:match("([%w]+)%s+(%d+)%s+(%d+)%s+([%w%p_]+)")
+    amplicons[ampName] = {chr=chr, startPos=tonumber(startPos), endPos=tonumber(endPos)}
+  end
+  return amplicons
+end
+
+-- updates the global header table with the entries
+local function processSamHeaderLine(l, amplicons)
+  if l:sub(1,3) == "@HD" then header.hd = l
+  elseif l:sub(1,3) == "@CO" then header.co = l
+  else
+    if not header.sq then header.sq = {} end
+    local ampName = l:match("@SQ%s+SN:ps%d+_([%w%p_]+).*")
+    local chr = amplicons[ampName].chr
+    header.sq[chr] = chrlength[chr]
+  end
+end
+
+local function printHeader()
+  if header.hd then headerFile:write(header.hd.."\n") else headerFile:write("@HD VN:PB_v0.1") end
+  for chr, len in pairs(header.sq) do
+    headerFile:write("@SQ\tSN:"..chr.."\tLN:"..len.."\n")
+  end
+  if header.co then headerFile:write(header.co.."\n") end
+end
+
+local function printReads()
+  for _, v in ipairs(reads) do bodyFile:write(v.."\n") end
+end
+
+
+local amplicons = readAmpliconFile()  -- amplicons indexed by name
+
+--for i,v in pairs(amplicons) do print("'"..i.."'") end
+
+for l in io.lines(samFile) do
+  if l:sub(1,1) == "@" then processSamHeaderLine(l, amplicons)
+  else
+    local before, amp, mapStart, after = l:match("(%d+%s+%d+%s+)ps%d+_([%w%p_]+)%s+(%d+)(.*)")
+    table.insert(reads, before..amplicons[amp].chr.."\t"..amplicons[amp].startPos + mapStart..after)
+  end
+end
+
+printHeader()
+printReads()
\ No newline at end of file