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Add a "recipes" page for the documentation, which provide tested examples of how to use BioSequences. Remove links to Gitter, and to OpenCollective.
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| ```@meta | ||
| CurrentModule = BioSequences | ||
| DocTestSetup = quote | ||
| using BioSequences | ||
| using BioSymbols | ||
| end | ||
| ``` | ||
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| ## Recipes | ||
| This page provides tested example code to solve various common problems using | ||
| BioSequences. | ||
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| ### One-hot encoding biosequences | ||
| The types `DNA`, `RNA` and `AminoAcid` expose a binary representation through | ||
| the exported function `BioSymbols.compatbits`, which is a one-hot encoding of: | ||
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| ```jldoctest | ||
| julia> using BioSymbols | ||
| julia> compatbits(DNA_W) | ||
| 0x09 | ||
| julia> compatbits(AA_J) | ||
| 0x00000600 | ||
| ``` | ||
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| Each set bit in the encoding corresponds to a compatible unambiguous symbol. | ||
| For example, for `RNA`, the four lower bits encode A, C, G, and U, in order. | ||
| Hence, the symbol `D`, which is short for A, G or U, is encoded as | ||
| `0x01 | 0x04 | 0x08 == 0x0d`: | ||
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| ```jldoctest | ||
| julia> compatbits(RNA_D) | ||
| 0x0d | ||
| julia> compatbits(RNA_A) | compatbits(DNA_G) | compatbits(RNA_U) | ||
| 0x0d | ||
| ``` | ||
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| Using this, we can construct a function to one-hot encode sequences - in this | ||
| example, nucleic acid sequences: | ||
| ```jldoctest | ||
| function one_hot(s::NucSeq) | ||
| M = falses(4, length(s)) | ||
| for (i, s) in enumerate(s) | ||
| bits = compatbits(s) | ||
| while !iszero(bits) | ||
| M[trailing_zeros(bits) + 1, i] = true | ||
| bits &= bits - one(bits) # clear lowest bit | ||
| end | ||
| end | ||
| M | ||
| end | ||
| one_hot(dna"TGNTKCTW-T") | ||
| # output | ||
| 4×10 BitMatrix: | ||
| 0 0 1 0 0 0 0 1 0 0 | ||
| 0 0 1 0 0 1 0 0 0 0 | ||
| 0 1 1 0 1 0 0 0 0 0 | ||
| 1 0 1 1 1 0 1 1 0 1 | ||
| ``` | ||
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