# Another question on eachoverlap in GenomicFeatures.jl

**URL:** <https://discourse.julialang.org/t/another-question-on-eachoverlap-in-genomicfeatures-jl/90426>\
**Category:** Biology, Health, and Medicine\
**Tags:** question\
**Created:** [November 18, 2022, 3:33am UTC](https://discourse.julialang.org/t/another-question-on-eachoverlap-in-genomicfeatures-jl/90426 "2022-11-18T03:33:12Z")\
**Posts on this page:** 1\
**Showing post:** 5

<div class="post-metadata">

**Author:** ![CiaranOMara](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/ciaranomara/32/2589_2.png) [@CiaranOMara](https://discourse.julialang.org/u/CiaranOMara)\
**Post date:** [November 27, 2022, 11:41pm UTC](https://discourse.julialang.org/t/another-question-on-eachoverlap-in-genomicfeatures-jl/90426/5 "2022-11-27T23:41:29Z")

</div>

Below is an example of how I would introduce a filtering step.  
Adjust the filtering step as required – your overlap criteria weren’t clear to me.

```julia
using GenomicFeatures #v2
using DataFrames

col = [
	Interval("chr1", 10628, 10683, '?', "abc")
	Interval("chr1", 10643, 10779, '?', "abc")
	Interval("chr1", 10645, 10748, '?', "abc")
	Interval("chr1", 10648, 10786, '?', "abc")
	Interval("chr1", 10676, 10767, '?', "abc")
	Interval("chr1", 10690, 10731, '?', "abc")
	Interval("chr1", 10707, 10793, '?', "abc")
	Interval("chr1", 10742, 10814, '?', "abc")
] |> IntervalCollection

hhh = [
	Interval("chr1", 10631, 10638)
	Interval("chr1", 10633, 10635)
	Interval("chr1", 10636, 10650)
	Interval("chr1", 10638, 10649)
	Interval("chr1", 10641, 10651)
	Interval("chr1", 10644, 10689)
	Interval("chr1", 10645, 10660)
	Interval("chr1", 10650, 10650)
] |> IntervalCollection

function number_interval(tp::Tuple)
	# Unpack Tuple.
	(i, interval) = tp

	# Setup numbered metadata.
	new_metadata = (
		i = i,
		original = GenomicFeatures.metadata(interval)
	)

	# Create new interval with numbered metadata.
	return Interval(
		seqname(interval),
		leftposition(interval),
		rightposition(interval),
		strand(interval),
		new_metadata
	)
end

"""
Given intervals a and b, that are assumed to overlap, the overlap is the span between the maximum left position and minimum right position.
interval: a b a b
    side: l l r r
  layout: |----|----|---|
"""
function overlap_span(interval_a, interval_b)
	left = max(leftposition(interval_a), leftposition(interval_b))
	right = min(rightposition(interval_a), rightposition(interval_b))
	return length(left:right)
end

# Convert intervals.
col_numbered = col |> enumerate .|> number_interval |> IntervalCollection
hhh_numbered = hhh |> enumerate .|> number_interval |> IntervalCollection

# Setup overlap iterator.
itr = eachoverlap(col_numbered, hhh_numbered); # Note: suppressing IntervalTree's output.

# Setup "on the fly" filtering.
itr = Iterators.filter(itr) do (c, h)
	# Select pairs with a minimum overlap of 5.
	if overlap_span(c, h) >= 5
		return true
	end
	
	# Reject overlapping pair.
	return false
end

# Setup result generator.
itr = Base.Generator(itr) do (c, h)
	result = (
		queryHits = GenomicFeatures.metadata(c).i,
		subjectHits = GenomicFeatures.metadata(h).i
	)
	return result
end

# Collect results in a `DataFrame`.
df = DataFrame(itr)

```

```julia
julia> df
19×2 DataFrame
 Row │ queryHits subjectHits 
     │ Int64 Int64       
─────┼────────────────────────
   1 │ 1 1
   2 │ 1 3
   3 │ 1 4
   4 │ 1 5
   5 │ 1 6
   6 │ 1 7
   7 │ 2 3
   8 │ 2 4
   9 │ 2 5
  10 │ 2 6
  11 │ 2 7
  12 │ 3 3
  13 │ 3 4
  14 │ 3 5
  15 │ 3 6
  16 │ 3 7
  17 │ 4 6
  18 │ 4 7
  19 │ 5 6

```

This question of [zhangchunyong](https://discourse.julialang.org/u/zhangchunyong)’s continues from the following.

> [@Some questions about eachoverlap in GenomicFeatures.jl](https://discourse.julialang.org/t/some-questions-about-eachoverlap-in-genomicfeatures-jl/85977/6):
>
> Thanks for helping me again.It works.Best wishes.

---

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