140 lines
5.5 KiB
Lua
140 lines
5.5 KiB
Lua
------------------------------------------------------------------------------------------------------------------------
|
|
-- Creates a new interval table
|
|
--
|
|
-- Return values:
|
|
-- 1: Interval table
|
|
------------------------------------------------------------------------------------------------------------------------
|
|
|
|
function newInterval(chr, start, finish, strand, info)
|
|
return {chr= chr, start=tonumber(start), finish=tonumber(finish), strand=strand, info=info}
|
|
end
|
|
|
|
|
|
------------------------------------------------------------------------------------------------------------------------
|
|
-- Parses a line from an interval list file (not a header line!)
|
|
--
|
|
-- Return values:
|
|
-- 1: chromosome
|
|
-- 2: interval start
|
|
-- 3: interval end
|
|
-- 4: strand (+/-)
|
|
-- 5: info field
|
|
------------------------------------------------------------------------------------------------------------------------
|
|
local function parseIntervalLine(l)
|
|
return l:match("(%w+)%s+(%d+)%s+(%d+)%s+([%+%-])%s+(.*)")
|
|
end
|
|
|
|
------------------------------------------------------------------------------------------------------------------------
|
|
-- Reads an interval list file into a table
|
|
--
|
|
-- Return values:
|
|
-- 1: table of intervals
|
|
-- 2: header string
|
|
------------------------------------------------------------------------------------------------------------------------
|
|
local function readIntervalList(filename)
|
|
t = {}
|
|
header = ""
|
|
for l in io.lines(filename) do
|
|
if l:sub(1,1) == "@" then header = header .. l .."\n"
|
|
else
|
|
local chr, start, finish, strand, info = parseIntervalLine(l)
|
|
table.insert(t, newInterval(chr, start, finish, strand, info))
|
|
end
|
|
end
|
|
return t, header
|
|
end
|
|
|
|
------------------------------------------------------------------------------------------------------------------------
|
|
-- Checks if two intervals have the same chromosome, start and end.
|
|
--
|
|
-- Return values:
|
|
-- 1: true/false
|
|
------------------------------------------------------------------------------------------------------------------------
|
|
local function isSameInterval (i1, i2)
|
|
return i1.chr == i2.chr and i1.start == i2.start and i1.finish == i2.finish
|
|
end
|
|
|
|
------------------------------------------------------------------------------------------------------------------------
|
|
-- Checks if the line from an interval list file is a header line
|
|
--
|
|
-- Return values:
|
|
-- 1: true/false
|
|
------------------------------------------------------------------------------------------------------------------------
|
|
local function isIntervalHeaderLine(l)
|
|
return l:sub(1,1) == "@"
|
|
end
|
|
|
|
|
|
------------------------------------------------------------------------------------------------------------------------
|
|
-- Compares the start position of two intervals
|
|
--
|
|
-- Return values:
|
|
-- 1: -1, 0 or 1 (respectively for a < b, a == b, a > b)
|
|
------------------------------------------------------------------------------------------------------------------------
|
|
local function compIntervals(a, b)
|
|
|
|
local function c(x,y)
|
|
if x < y then return -1
|
|
elseif x > y then return 1
|
|
else return 0 end
|
|
end
|
|
-- same chromosomes
|
|
if a.chr == b.chr then return c(a.start, b.start)
|
|
else
|
|
x = tonumber(a.chr)
|
|
y = tonumber(b.chr)
|
|
if x and y then return c(x,y)
|
|
else return c(a.chr, b.chr) end
|
|
end
|
|
end
|
|
|
|
------------------------------------------------------------------------------------------------------------------------
|
|
-- Compare function to sort a list of intervals (use with table.sort)
|
|
--
|
|
-- Return values:
|
|
-- 1: true if a < b, false otherwise.
|
|
------------------------------------------------------------------------------------------------------------------------
|
|
local function sortCompInterval(a, b)
|
|
if a.chr == b.chr then return a.start < b.start end
|
|
local x = tonumber(a.chr)
|
|
local y = tonumber(b.chr)
|
|
if x and y then
|
|
return x < y end
|
|
return a.chr < b.chr
|
|
end
|
|
|
|
------------------------------------------------------------------------------------------------------------------------
|
|
-- Checks if the interval is a valid human genome interval
|
|
--
|
|
-- Return values:
|
|
-- 1: true/false
|
|
------------------------------------------------------------------------------------------------------------------------
|
|
local function isValidInterval(interval)
|
|
local x
|
|
if interval.chr == "X" then x = 23
|
|
elseif interval.chr == "Y" then x = 24
|
|
elseif interval.chr == "MT" then x = 25
|
|
else x = tonumber(interval.chr) end
|
|
return x >= 1 and x <= 25 and interval.start < interval.finish and chr_limits[x] > interval.finish
|
|
end
|
|
|
|
|
|
------------------------------------------------------------------------------------------------------------------------
|
|
-- Checks if the intervals are overlapping. Intervals are said to overlap if one of the following is true:
|
|
-- i1i2: i1 starts before i2, but ends inside i2.
|
|
-- i2i1: i2 starts before i1, but ends inside i1.
|
|
-- i1_inside: i1 is fully contained inside i2.
|
|
-- i2_inside: i2 is fully contained inside i1.
|
|
--
|
|
-- Return values:
|
|
-- 1: true/false
|
|
-- 2: if true, returns "i1i2", "i2i1", "i1_inside", "i2_inside"
|
|
------------------------------------------------------------------------------------------------------------------------
|
|
local function isOverlappingInterval(i1, i2)
|
|
if i1.chr ~= i2.chr then return false
|
|
elseif i1.start < i2.start and i1.finish < i2.finish then return true, "i1i2"
|
|
elseif i2.start < i1.start and i2.finish < i1.finish then return true, "i2i1"
|
|
elseif i1.start > i2.start and i1.finish < i2.finish then return true, "i1_inside"
|
|
elseif i2.start > i1.start and i2.finish < i1.finish then return true, "i2_inside"
|
|
else return false end
|
|
end |