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Nim for Bioinformatics

Tuples

Table of contents

  1. Tuples
    1. An example

Tuples

Arrays and sequences are homogeneous lists, while tuples can store a fixed-size list of hetherogeneous variables.

let mixedItems = ("Nim", 42, 0.33)
echo mixedItems[1]                    # will print 42

What makes tuples very nice to use, is that you can name each item:

var
  ctgStats: tuple[name: string, size: int, coverage: float]
  thisCtgStats = (name: "Contig1", size: 1400, coverage: 12.44)

# Access items and edit them:
echo thisCtgStats.name, " size is ", thisCtgStats.size, " bp."
thisCtgStats.name = "Contig_1"

An example

Here we use a tuple to create a custom type (ctgInfo) to store three properties of an assembled contig (the name, the coverage and its length)

# new type that is a tuple
type
    ctgInfo = tuple[name: string, cov: float, length: int]

# You can create a sequence of type 'ctgInfo'
var
  contigs = newSeq[ctgInfo]()

# Create some instances and make a sequence
var
    p1: ctgInfo = (name: "p1", cov: 60.0, length: 10)
    p2: ctgInfo = (name: "p2", cov: 20.0, length: 10)
    p3: ctgInfo = (name: "p3", cov: 30.0, length: 10)
    p4: ctgInfo = (name: "p4", cov: 30.0, length: 10)
    assembly = @[p1,p2,p4,p3]

# Or add tuples to the Sequences sequence
contigs.add((name: "p24", cov: 2990.0, length: 10))
contigs.add((name: "p41", cov: 30.0, length: 10))
contigs.add((name: "p94", cov: 300.0, length: 210))

# Print the sequence
echo "Contigs: ", assembly

# Loop the sequence
for ctg in assembly:
  echo ctg.name, "\t", ctg.cov, "X", "\tlen=", ctg.length, " bp"

The output will be:

Contigs sequence: @[(name: "p1", cov: 60.0, length: 10), (name: "p2", cov: 20.0, length: 10), (name: "p4", cov: 30.0, length: 10), (name: "p3", cov: 30.0, length: 10)]
p1  60.0X   len=10 bp
p2  20.0X   len=10 bp
p4  30.0X   len=10 bp
p3  30.0X   len=10 bp