Bioinformatics/Sequence mutation: Difference between revisions

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type

# Enumeration type for bases.

Base {.pure.} = enum A, C, G, T, Other = "other"

# Sequence of bases.

DnaSequence = ~~seq[Base]~~

DnaSequence = string

# Kind of mutation.

Mutation = enum mutSwap, mutDelete, mutInsert

const MaxBaseVal = ord(Base.high) - 1 # Maximum base value.

#---------------------------------------------------------------------------------------------------

template toChar(base: Base): char = ($base)[0]

#---------------------------------------------------------------------------------------------------

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## Create a DNA sequence of given length.

result = ~~newSeqOfCap[Base]~~(length)

result = newStringOfCap(length)

for _ in 1..length:

result.add(Base(rand(3)))

result.add($Base(rand(MaxBaseVal)))

#---------------------------------------------------------------------------------------------------

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let newBase = Base(rand(ord(Base.Other) - 1))

echo fmt"Changing base at position {idx + 1} from {dnaSeq[idx]} to {newBase}"

dnaSeq[idx] = newBase

dnaSeq[idx] = newBase.toChar

of mutDelete:

echo fmt"Deleting base {dnaSeq[idx]} at position {idx + 1}"

dnaSeq.delete(idx)

dnaSeq.delete(idx, idx)

of mutInsert:

let newBase = Base(rand(ord(Base.Other) - 1))

echo fmt"Inserting base {newBase} at position {idx + 1}"

dnaSeq.insert(newBase, idx)

dnaSeq.insert($newBase, idx)

#---------------------------------------------------------------------------------------------------

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var counts: array[Base, Natural] # Count of bases.

for ~~base~~ in dnaSeq:

for c in dnaSeq:

inc counts[~~base~~]

inc counts[parseEnum[Base]($c, Other)] # Use Other as default value.

# Display the SQ line.