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Nim for Bioinformatics

Tables

Table of contents

  1. Ordered tables
  2. Count tables

Tables are sequences of pairs, and they are similar to what other languages call hashes, associative arrays or dictionaries, but they require a library to be imported to be used (tables).

:information: In my opinion, tables are less needed in nim if compared with other languages, as a custom type will probably prove to be a good alternative. See next chapter.

Nim tables are typed, but keys and values can have a different type. As usual let’s see how to declare an empty table and how to initialize a table with an assignment:

# You need to import the 'tables' library first
import tables

# create a new Table with and without data assignment
var
  cuttingPosition : initTable[string, int]()
  motifs = {"EcoRI": "GAATTC", "HindIII": "AAGCTT"}.toTable  

# Add a key/value pair:
motifs["HpaI"] = "GTTAAC"
cuttingPosition["HpaI"] = 3

Ordered tables

A table will not keep its item ordered (unlike arrays and sequences), but if for some reasons the insertion order matters, ordered tables are the solution. Instead of using Table[A, B] type, you will use the OrderedTable[A, B] type.

Count tables

A CountTable initialise a counter for each key, that can be incremented by 1 or another integer:

var
  SequenceCounts = initCountTable[string]()

# to increase of 1
SequenceCounts.inc("GATTACA")

# to increase of 10
SequenceCounts.inc("TATA", 10)