mirror of
https://github.com/MillironX/SequenceVariation.jl.git
synced 2024-11-22 13:29:56 +00:00
35 lines
1.1 KiB
Julia
35 lines
1.1 KiB
Julia
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"""
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Needs to be able to:
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* Given a sequence and a reference, create a `Variant` that unambiguously represents
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the sequence
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* Given a `Variant` and a new reference, translate the variant to the new reference.
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* Given a mutation and a reference and a sequence, determine if the sequence has that
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mutation
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TODO now:
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* Create a string repr and parser for Edit, perhaps
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* A243T for sub
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* 119TAGGCTA for insertion
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* TGAGCTA9 for deletion
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* Create a parser + print/show for edit
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* Play around with some NGS results rel. to picked reference.
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* Is it easy to construct ref and variants? I.e. is API nice?
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* Is it nice and easy to check if a mut is present?
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*
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* Implement "reference switching".
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* Add tests
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"""
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using BioSequences
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using BioAlignments
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using SequenceVariation
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const DNA_MODEL = BioAlignments.AffineGapScoreModel(EDNAFULL, gap_open=-25, gap_extend=-2)
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align(a::BioSequence, b::BioSequence) = pairalign(GlobalAlignment(), a, b, DNA_MODEL).aln
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seq1 = ungap!(dna"--ATGCGTGTTAGCAAC--TTATCGCG")
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seq2 = ungap!(dna"TGATGCGTGT-AGCAACACTTATAGCG")
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var = Variant(align(seq1, seq2))
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