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Update documentation wording to reflect new type names
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4 changed files with 26 additions and 25 deletions
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@ -4,7 +4,7 @@ CurrentModule = SequenceVariation
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# Comparing variations in sequences
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## Checking for variations in a known variant
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## Checking for variations in a known haplotype
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Looking for a known [`Variation`](@ref) within a [`Haplotype`](@ref) is
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efficiently accomplished using the `in` operator.
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@ -21,27 +21,27 @@ bos_ovis_alignment =
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bos_human_alignment =
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PairwiseAlignment(AlignedSequence(human, Alignment("32M", 1, 1)), bovine);
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bos_ovis_variant = Haplotype(bos_ovis_alignment)
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bos_human_variant = Haplotype(bos_human_alignment)
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bos_ovis_haplotype = Haplotype(bos_ovis_alignment)
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bos_human_haplotype = Haplotype(bos_human_alignment)
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```
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```@example call_variants
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println("\tOvis aires\tHomo sapiens")
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for v in vcat(variations(bos_ovis_variant), variations(bos_human_variant))
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is_sheep = v in bos_ovis_variant
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is_human = v in bos_human_variant
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for v in vcat(variations(bos_ovis_haplotype), variations(bos_human_haplotype))
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is_sheep = v in bos_ovis_haplotype
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is_human = v in bos_human_haplotype
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println("$v\t$is_sheep\t\t$is_human")
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end
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```
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## Constructing new variants based on other variations
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## Constructing new haplotypes based on other variations
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New variants can be constructed using variations. This might be useful to pool
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variations found on different reads or to filter variations from a variant
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that aren't validated by another variant.
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New haplotypes can be constructed using variations. This might be useful to pool
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variations found on different reads or to filter variations from a haplotype
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that aren't validated by another haplotype.
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```@repl call_variants
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sheeple = vcat(variations(bos_ovis_variant), variations(bos_human_variant));
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sheeple = vcat(variations(bos_ovis_haplotype), variations(bos_human_haplotype));
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Haplotype(bovine, sheeple)
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reconstruct!(bovine, ans)
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```
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@ -2,13 +2,14 @@
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CurrentModule = SequenceVariation
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```
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# Working with variants
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# Working with haplotypes
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## Calling variants
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The first step in working with sequence variation is to identify (call)
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variations. SequenceVariation can directly call variants using the
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`Haplotype(::PairwiseAlignment)` constructor of the [`Haplotype`](@ref) type.
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variations between two sequences. SequenceVariation can directly call variants
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using the `Haplotype(::PairwiseAlignment)` constructor of the
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[`Haplotype`](@ref) type.
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```@repl call_variants
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using SequenceVariation, BioAlignments, BioSequences
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@ -22,19 +23,19 @@ bos_ovis_alignment =
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bos_human_alignment =
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PairwiseAlignment(AlignedSequence(human, Alignment("32M", 1, 1)), bovine);
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bos_ovis_variant = Haplotype(bos_ovis_alignment)
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bos_human_variant = Haplotype(bos_human_alignment)
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bos_ovis_haplotype = Haplotype(bos_ovis_alignment)
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bos_human_haplotype = Haplotype(bos_human_alignment)
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```
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## Sequence reconstruction
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If the alternate sequence of a variant is no longer available (as is often the
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If the alternate sequence of a haplotype is no longer available (as is often the
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case when calling variants from alignment files), then the sequence can be
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retrieved using the [`reconstruct!`](@ref) function.
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```@repl call_variants
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human2 = copy(bovine);
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reconstruct!(human2, bos_human_variant)
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reconstruct!(human2, bos_human_haplotype)
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human2 == bovine
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human2 == human
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```
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@ -42,13 +42,13 @@ bos_ovis_alignment =
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bos_human_alignment =
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PairwiseAlignment(AlignedSequence(human, Alignment("32M", 1, 1)), bovine);
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bos_ovis_variant = Haplotype(bos_ovis_alignment)
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bos_human_variant = Haplotype(bos_human_alignment)
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bos_ovis_haplotype = Haplotype(bos_ovis_alignment)
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bos_human_haplotype = Haplotype(bos_human_alignment)
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```
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```@repl call_variants
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variations(bos_ovis_variant)
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variations(bos_human_variant)
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variations(bos_ovis_haplotype)
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variations(bos_human_haplotype)
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```
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## Reference switching
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@ -59,8 +59,8 @@ alignment between the new and old references using the [`translate`](@ref).
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```@repl call_variants
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ovis_human_alignment =
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PairwiseAlignment(AlignedSequence(human, Alignment("32M", 1, 1)), ovine)
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human_variation = first(variations(bos_ovis_variant))
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human_variation = first(variations(bos_ovis_haplotype))
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reference(ans) == bovine
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SequenceVariation.translate(human_variation, ovis_human_alignment)
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SequenceVariation.translate(human_variation, ovis_human_haplotype)
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reference(ans) == bovine
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```
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@ -2,7 +2,7 @@
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Haplotype{S<:BioSequence,T<:BioSymbol}
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A set of variations within a given sequence that are all found together. Depending on the
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field, it might also be referred to as a "genotype," "haplotype," or "strain."
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field, it might also be referred to as a "genotype" or "strain."
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# Constructors
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