genomisc

README

genomisc

Miscellaneous genomics tools and data structures in golang

HWE

go get github.com/carbocation/genomisc/hwe

HWE computes Exact or Approximate Hardy-Weinberg P value. Fast computes the approximate P value, then if it is significant according to your threshold, it computes the Exact P-value to be certain. This is a pure go implementation with naive algorithms, which can therefore be slow. It uses big.Int and can handle extremely large sample sizes (~hundreds of thousands).

RAMCSV

go get github.com/carbocation/genomisc/ramcsv

RAMCSV consumes a file handle and a csv.Reader (which exists only to provide your csv parsing settings) and allows you to seek back and forth through a CSV file to any line in the file, without having to actually keep the full file in memory.

PRSParser

go get github.com/carbocation/genomisc/prsparser

PRSParser consumes a variety of formats for polygenic scores.

Documentation

Index

• Constants
• func DetermineDelimiter(r io.Reader) rune
• func ExpandHome(path string) string
• func MaybeDecompressReadCloserFromFile(f io.ReadSeekCloser) (io.ReadCloser, error)
• func MaybeOpenSeekerFromGoogleStorage(path string, client *storage.Client) (io.ReadSeekCloser, error)
• type BIM
  • func OpenBIM(path string) (*BIM, error)
  • func (b *BIM) Close() error
  • func (b *BIM) Err() error
  • func (b *BIM) Read() *BIMRow
• type BIMRow
• type DataType
  • func DetectDataType(r io.Reader) (DataType, error)
• type GSReadSeekCloser
  • func (o *GSReadSeekCloser) Close() error
  • func (s *GSReadSeekCloser) Read(buf []byte) (int, error)
  • func (s *GSReadSeekCloser) Seek(offset int64, whence int) (int64, error)
• type GSReaderAtCloser
  • func (o *GSReaderAtCloser) Close() error
  • func (o *GSReaderAtCloser) Read(p []byte) (n int, err error)
  • func (o *GSReaderAtCloser) ReadAt(p []byte, offset int64) (n int, err error)
• type ReaderAtCloser

Constants

const (
	Chromosome int = iota
	VariantID
	Morgans
	Coordinate
	Allele1
	Allele2
)

Map columns in the BIM file to their positions

Functions

func DetermineDelimiter

func DetermineDelimiter(r io.Reader) rune

DetermineDelimiter returns the single most likely rune that would delimit the values in the reader, assuming a CSV-like file.

func ExpandHome

func ExpandHome(path string) string

ExpandHome expands ~ to its proper path, where appropriate.

func MaybeDecompressReadCloserFromFile

func MaybeDecompressReadCloserFromFile(f io.ReadSeekCloser) (io.ReadCloser, error)

MaybeDecompressReadCloserFromFile detects whether a file-like object (must implement io.Reader, io.Seeker, and io.Closer) is compressed with GZip, Zip, BZip2, XZ, or Z and decompresses it. If not, it returns the file as-is. It uses the seek method to ensure that the reader is reset to the starting byte so that it does not discard bytes.

func MaybeOpenSeekerFromGoogleStorage

func MaybeOpenSeekerFromGoogleStorage(path string, client *storage.Client) (io.ReadSeekCloser, error)

Types

type BIM

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

func OpenBIM

func OpenBIM(path string) (*BIM, error)

func (*BIM) Close

func (b *BIM) Close() error

func (*BIM) Err

func (b *BIM) Err() error

func (*BIM) Read

func (b *BIM) Read() *BIMRow

type BIMRow

type BIMRow struct {
	Chromosome string
	Coordinate uint32 // Labeled "position" by most applications
	VariantID  string // E.g., RSID
	Allele1    string // Can contain > 1 character
	Allele2    string // Can contain > 1 character

}

type DataType

type DataType byte

const (
	DataTypeInvalid DataType = iota
	DataTypeNoCompression
	DataTypeGzip
	DataTypeZip
	DataTypeXZ
	DataTypeZ
	DataTypeBZip2
)

func DetectDataType

func DetectDataType(r io.Reader) (DataType, error)

DetectDataType attempts to detect the data type of a stream by checking against a set of known data types. Byte code signatures from https://stackoverflow.com/a/19127748/199475

type GSReadSeekCloser

type GSReadSeekCloser struct {
	*storage.ObjectHandle
	Context context.Context
	Closer  *func() error
	// contains filtered or unexported fields
}

Decorates a Google Storage object handle with an io.ReadSeekCloser. Derived from https://github.com/googleapis/google-cloud-go/issues/1124#issuecomment-419070541

func (*GSReadSeekCloser) Close

func (o *GSReadSeekCloser) Close() error

Satisfies io.Closer. If o.close is not set, this is a nop.

func (*GSReadSeekCloser) Read

func (s *GSReadSeekCloser) Read(buf []byte) (int, error)

func (*GSReadSeekCloser) Seek

func (s *GSReadSeekCloser) Seek(offset int64, whence int) (int64, error)

type GSReaderAtCloser

type GSReaderAtCloser struct {
	*storage.ObjectHandle
	Context context.Context
	Closer  *func() error
	Reader  *storage.Reader
}

Decorates a Google Storage object handle with ReadAt

func (*GSReaderAtCloser) Close

func (o *GSReaderAtCloser) Close() error

Satisfies io.Closer. If o.close is not set, this is a nop.

func (*GSReaderAtCloser) Read

func (o *GSReaderAtCloser) Read(p []byte) (n int, err error)

func (*GSReaderAtCloser) ReadAt

func (o *GSReaderAtCloser) ReadAt(p []byte, offset int64) (n int, err error)

ReadAt satisfies io.ReaderAt. Note that this is dependent upon making p a buffer of the desired length to be read by NewRangeReader.

type ReaderAtCloser

type ReaderAtCloser interface {
	io.Reader
	io.ReaderAt
	io.Closer
}