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--[[
Copyright (c) 2007-2008 Gordon Gremme <gordon@gremme.org>
Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg
Permission to use, copy, modify, and distribute this software for any
purpose with or without fee is hereby granted, provided that the above
copyright notice and this permission notice appear in all copies.
THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
]]
module(..., package.seeall)
require "gtlua.genome_features"
-- XXX: remove if statement if libannotationsketch is always compiled in
if GenomeTools_feature_index then
-- Computes the coverage for the sequence ID <seqid>. The optional <maxdist>
-- parameter denotes the maximal distance two features can be apart without
-- creating a new Range. Returns an array of Ranges denoting parts the of
-- <seqid> covered by features.
function GenomeTools_feature_index:get_coverage(seqid, maxdist)
assert(seqid)
local maxdist = maxdist or 0
local features = self:get_features_for_seqid(seqid)
local starpos, endpos
local minstartpos = nil
local maxendpos = nil
local ranges = {}
local coverage = {}
-- collect all feature ranges
for i, feature in ipairs(features) do
ranges[#ranges+1] = feature:get_range()
end
-- sort feature ranges
ranges = gt.ranges_sort(ranges)
-- compute and store coverage
for i, range in ipairs(ranges) do
startpos, endpos = range:get_start(), range:get_end()
if i == 1 then
minstartpos = startpos
maxendpos = endpos
else
-- assert(startpos >= minstartpos)
if (startpos > maxendpos + maxdist) then
-- new region started
coverage[#coverage+1] = gt.range_new(minstartpos, maxendpos)
minstartpos = startpos
maxendpos = endpos
else
-- continue old region
maxendpos = (endpos > maxendpos) and endpos or maxendpos
end
end
end
-- add last region
coverage[#coverage+1] = gt.range_new(minstartpos, maxendpos)
return coverage
end
-- Returns an array of Ranges denoting parts of <seqid> which are covered by
-- at least one marked feature. Internally, get_coverage() is called and the
-- <maxdist> is passed along.
function GenomeTools_feature_index:get_marked_regions(seqid, maxdist)
assert(seqid, "missing seqid argument")
local coverage = self:get_coverage(seqid, maxdist)
local marked = {}
for _,range in ipairs(coverage) do
local features = feature_index:get_features_for_range(seqid, range)
if gt.features_contain_marked(features) then
marked[#marked+1] = range
end
end
return marked
end
-- Render to PNG file <png_file> for <seqid> in <range> with optional <width>.
-- If no <png_file> is given os.tmpname() is called to create one.
-- Returns name of written PNG file.
function GenomeTools_feature_index:render_to_png(seqid, range, png_file, width)
assert(seqid and range)
png_file = png_file or os.tmpname()
if not width then width = 1600 end
local diagram = gt.diagram_new(self, seqid, range)
local render = gt.render_new()
render:to_png(diagram, png_file, width)
return png_file
end
-- Show all sequence IDs.
function GenomeTools_feature_index:show_seqids()
for _,seqid in ipairs(feature_index:get_seqids()) do
print(seqid)
end
end
-- Returns all features from <feature_index>.
function GenomeTools_feature_index:get_all_features()
local seqids = self:get_seqids()
local all_features = {}
for _, seqid in ipairs(seqids) do
local seqid_features = self:get_features_for_seqid(seqid)
for _, feature in ipairs(seqid_features) do
all_features[#all_features + 1] = feature
end
end
return all_features
end
end
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