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Nim for Bioinformatics

Control flow

Table of contents

  1. Conditionals
  2. While
  3. For

This page briefly present the syntax for common control-flow patterns. Some more details can be presented in the worked examples.

Conditionals

To execute a set of statements if a condition is satistisfied. “If statements” in Nim have the typical Python-like structure as in the following example:

let firstLine = ">Sequence1"

if firstLine[0] == '>':
  echo "A nice FASTA file!"
elif firstLine[0] == '@':
  echo "A FASTQ record"
else:
  echo "ERROR: unrecognized format :("

Interestingly, if statements return the value of the expression they evaluate to, so you can mimicry a ternary operator like this:

# If MinLen > 0 then assign true, else assign false (to TruncateSeq)
var TuncateSeq = if MinLen > 0: true
               else: false

While

This loop will be execute while a condition is satisfied. It’s used when you do not know in advance when to stop.

while sumLen < halfGenome:
  let CtgSize = getNextContig()
  sumLen += CtgSize

For

For loops will repeat a set of instructions a defined number of times (or one time for each element of a set). For loops are very useful to iterate arrays and sequences, so more examples will be presented there.

for i in countup(1, 10):
  echo i, "..."

The countup function returns a list of integer starting from the first (in the example 1) to the last (in the example 10). The .. iterator is also commonly used, and it’s important to surround it by spaces (including its ..< variant):

# This will iterate from 1 to 10 (included)
for i in 1 .. 10:
  echo "inclusive: ", i

# This will iterate from 1 to 9 (included)
for i in 1 ..< 10:
  echo "exclusive: ", i