g-thomson / nimbioseq

Nim Library for sequence (protein/nucleotide) bioinformatics

Module nimbioSeq

Imports

sequtils, strutils, math, tables, osproc, streams

Types

Record = object

id*: string

description*: string

quality*: string

sequence*: string

This type represents a genetic sequence with optional quality

Procs

proc reverseComplement(self: Record): Record {..}

proc toFasta(self: Record; lineLength = 60): string {..} returns FASTA formatted string of sequence record

proc qualToChar(q: int): char {..} returns character for a given Illumina quality score

proc charToQual(c: char): int {..} returns Illumina quality score for a given character

proc toFastq(self: Record; qualityValue = 30): string {..} returns FASTQ formatted string of sequence record with given quality value to be applied to sequence

proc length(self: Record): int {..} returns length of sequence

proc kmer2num(kmer: string): int {..} converts a kmer string into an integer 0..4^(len-1)

proc num2kmer(num, klen: int): string {..} converts an integer into a kmer string given the number and length of kmer

proc toKmerFrequency(self: Record; klen: int; includeComplement = false): seq[int] {..} returns (overlapping) kmer frequencies of a nucleotide sequence

proc gc(self: Record): int {..} returns the number of bases that are G or C

proc ambiguous(self: Record): int {..} returns the number of bases that are not AGCTU

proc translate(self: Record; code = 1): Record {..} translates a nucleotide sequence with the given genetic code number

Iterators

iterator compressedLines(filename: string): string {..} iterator to read lines of a (maybe) compressed text file transparently

iterator readFasta(filename: string): Record {..} iterator to iterate over the FASTA records in a file

iterator readFastq(filename: string): Record {..} iterator to iterate over the FASTQ records in a file

iterator readSeqs(filename: string): Record {..}