pileup

Documentation

Overview

Package pileup contains pileup parsers and writers.

The pileup format is a text-based bioinformatics format to summarize aligned reads against a reference sequence. In comparison to simply getting a consensus sequence from sequencing data, pileup files can contain more context about the mutations in a sequencing run, which is especially useful when analyzing plasmid sequencing data from Nanopore sequencing runs.

Pileup files are basically tsv files with 6 columns: Sequence Identifier, Position, Reference Base, Read Count, Read Results, and Quality. An example from wikipedia (https://en.wikipedia.org/wiki/Pileup_format) is shown below:

```
seq1 	272 	T 	24 	,.$.....,,.,.,...,,,.,..^+. 	<<<+;<<<<<<<<<<<=<;<;7<&
seq1 	273 	T 	23 	,.....,,.,.,...,,,.,..A 	<<<;<<<<<<<<<3<=<<<;<<+
seq1 	274 	T 	23 	,.$....,,.,.,...,,,.,... 	7<7;<;<<<<<<<<<=<;<;<<6
seq1 	275 	A 	23 	,$....,,.,.,...,,,.,...^l. 	<+;9*<<<<<<<<<=<<:;<<<<
seq1 	276 	G 	22 	...T,,.,.,...,,,.,.... 	33;+<<7=7<<7<&<<1;<<6<
seq1 	277 	T 	22 	....,,.,.,.C.,,,.,..G. 	+7<;<<<<<<<&<=<<:;<<&<
seq1 	278 	G 	23 	....,,.,.,...,,,.,....^k. 	%38*<<;<7<<7<=<<<;<<<<<
seq1 	279 	C 	23 	A..T,,.,.,...,,,.,..... 	75&<<<<<<<<<=<<<9<<:<<<
```

1. Sequence Identifier: The sequence identifier of the reference sequence
2. Position: Position of row in the reference sequence (indexed at 1)
3. Reference Base: Base pair in reference sequence
4. Read Count: Number of aligned reads to this particular base pair
5. Read Results: The resultant alignments
6. Quality: Phred quality scores associated with each base

This package provides a parser and writer for working with pileup files.

Index

• func Write(pileups []Pileup, path string) error
• func WritePileups(pileups []Pileup, w io.Writer) error
• type Parser
  • func NewParser(r io.Reader, maxLineSize int) *Parser
  • func (parser *Parser) ParseAll() ([]Pileup, error)
  • func (parser *Parser) ParseN(maxRows int) (pileups []Pileup, err error)
  • func (parser *Parser) ParseNext() (Pileup, error)
  • func (parser *Parser) Reset(r io.Reader)
• type Pileup
  • func Parse(r io.Reader) ([]Pileup, error)
  • func Read(path string) ([]Pileup, error)

Functions

func Write

func Write(pileups []Pileup, path string) error

Write writes a pileup array to a file

func WritePileups

func WritePileups(pileups []Pileup, w io.Writer) error

WritePileups writes a pileup array to an io.Writer

Types

type Parser

type Parser struct {
	// contains filtered or unexported fields
}

Parser is a pileup parser.

func NewParser

func NewParser(r io.Reader, maxLineSize int) *Parser

NewParser creates a parser from an io.Reader for pileup data.

func (*Parser) ParseAll

func (parser *Parser) ParseAll() ([]Pileup, error)

ParseAll parses all sequences in underlying reader only returning non-EOF errors. It returns all valid pileup sequences up to error if encountered.

func (*Parser) ParseN

func (parser *Parser) ParseN(maxRows int) (pileups []Pileup, err error)

ParseN parses up to maxRows pileup sequences from the Parser's underlying reader. ParseN does not return EOF if encountered. If an non-EOF error is encountered it returns it and all correctly parsed sequences up to then.

func (*Parser) ParseNext

func (parser *Parser) ParseNext() (Pileup, error)

ParseNext parses the next pileup row in a pileup file. ParseNext returns an EOF if encountered.

func (*Parser) Reset

func (parser *Parser) Reset(r io.Reader)

Reset discards all data in buffer and resets state.

type Pileup

type Pileup struct {
	Sequence      string   `json:"sequence"`
	Position      uint     `json:"position"`
	ReferenceBase string   `json:"reference_base"`
	ReadCount     uint     `json:"read_count"`
	ReadResults   []string `json:"read_results"`
	Quality       string   `json:"quality"`
}

Pileup struct is a single position in a pileup file. Pileup files "pile" a bunch of separate bam/sam alignments into something more readable at a per base pair level, so are only useful as a grouping.

func Parse

func Parse(r io.Reader) ([]Pileup, error)

Parse parses a given Pileup file into an array of Pileup structs.

func Read

func Read(path string) ([]Pileup, error)

Read reads a file into an array of Pileup structs