genomisc

package module
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 Go to latest Published: Jul 26, 2024 License: BSD-3-Clause Imports: 18 Imported by: 2

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

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

Map columns in the BIM file to their positions

Variables

This section is empty.

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
}

Source Files

View all Source files

Directories

Path Synopsis
prsworker
tasker
cmd
animategcp command
animateunjitter command
animateunjitter removes lines from a sorted manifest in a fashion that avoids returning to a previously seen series_number.
 animateunjitter removes lines from a sorted manifest in a fashion that avoids returning to a previously seen series_number.
animatezip command
applyprsbasic command
applyprsgcp/prsreducer command
applyprsgcp/prsworker command
applyprsgcp/tasker command
batcher command
bgen2bigquery command
bgenreadsnp command
bgenreadsnp/allelecount command
bimfixduplicatesnpids command
bimmanglesnpids command
bimmanglesnpids is designed to handle a specific situation where you want to mangle rsids intentionally.
 bimmanglesnpids is designed to handle a specific situation where you want to mangle rsids intentionally.
bolt2ldhub command
Convert BOLT-LMM input into input satisfactory for ldhub
 Convert BOLT-LMM input into input satisfactory for ldhub
cardiaccycle command
cardiaccyclev2 command
clinvartab2bigquery command
clinvar2bigquery is designed to take clinvar data, filter it using criteria that are useful to my line of work, and then format it so that it can be ingested in bigquery.
 clinvar2bigquery is designed to take clinvar data, filter it using criteria that are useful to my line of work, and then format it so that it can be ingested in bigquery.
combine-spreadsheet command
critic/cmd/critic command
critic/web command
deleteunknown command
Deletes files from `folder` not matching names found in `permitted-list`, with `suffix` optionally being appended to `permitted-list` to facilitate matching.
 Deletes files from `folder` not matching names found in `permitted-list`, with `suffix` optionally being appended to `permitted-list` to facilitate matching.
dicom-mip command
dicom-mip produces maximum intensity projections, as well as average intensity projections and .mp4 videos of the projections through the 3D block of voxels from sagittal and coronal projections.
 dicom-mip produces maximum intensity projections, as well as average intensity projections and .mp4 videos of the projections through the 3D block of voxels from sagittal and coronal projections.
dicom2las command
dicom2las converts DICOM files to LAS files (LASer format), which is a [format for point clouds](https://en.wikipedia.org/wiki/LAS_file_format).
 dicom2las converts DICOM files to LAS files (LASer format), which is a [format for point clouds](https://en.wikipedia.org/wiki/LAS_file_format).
dicom2png command
dicomdump command
dicomvenc command
enhanceratlas/enhancergene command
gene2chrpos command
gene2chrpos/grch38 command
genes2sites command
MendelOverlap performs permutation to quantify surprise at the number of GWAS loci that overlap with Mendelian genes for your trait of interest.
 MendelOverlap performs permutation to quantify surprise at the number of GWAS loci that overlap with Mendelian genes for your trait of interest.
gtf2tsv command
gtf2tsv flattens a gtf file to a tsv seems to require a 2-pass approach
 gtf2tsv flattens a gtf file to a tsv seems to require a 2-pass approach
interpolatecm command
liftover command
locusid command
mendeloverlap command
MendelOverlap performs permutation to quantify surprise at the number of GWAS loci that overlap with Mendelian genes for your trait of interest.
 MendelOverlap performs permutation to quantify surprise at the number of GWAS loci that overlap with Mendelian genes for your trait of interest.
nearbygenes command
nearbygenes finds all genes whose transcript start sites are within a given radius of a given chr:pos.
 nearbygenes finds all genes whose transcript start sites are within a given radius of a given chr:pos.
nearestgene command
nearestgene finds the single gene whose transcript start site is closest to a given chr:pos.
 nearestgene finds the single gene whose transcript start site is closest to a given chr:pos.
nifti2png command
pixelcounter command
pixeloverlap command
pixeloverlap computes overlap/agreement metrics between two images drawn with an encoding compatible with the overlay.LabeledPixelToID function.
 pixeloverlap computes overlap/agreement metrics between two images drawn with an encoding compatible with the overlay.LabeledPixelToID function.
pixeloverlapsummary command
pixeloverlapsummary is a convenience tool to summarize the output of pixeloverlap by label
 pixeloverlapsummary is a convenience tool to summarize the output of pixeloverlap by label
pixelqc command
colqc performs qc on columnar data (the output of pixelcounter)
 colqc performs qc on columnar data (the output of pixelcounter)
pixelreplace command
pixelreplace replaces specific pixel-label IDs from the overlay package with specified replacement labels.
 pixelreplace replaces specific pixel-label IDs from the overlay package with specified replacement labels.
pngaverage command
pngnorms command
pngoverlay command
pngreplace command
pngreplace replaces specific pixel-labels from the overlay package with specified replacement labels.
 pngreplace replaces specific pixel-labels from the overlay package with specified replacement labels.
pngtostack command
pngupsample command
pngupsample ingests a PNG and parameters that indicate (1) how to resize pixels and (2) which subset of the image to upsample, then produces the subsetted, upsampled PNG.
 pngupsample ingests a PNG and parameters that indicate (1) how to resize pixels and (2) which subset of the image to upsample, then produces the subsetted, upsampled PNG.
printdisease command
rawdicom2png command
regenie2bolt command
regenie2exponent command
saige2bolt command
ukbb2csv/censor command
ukbb2csv/convertcoding command
ukbb2csv/convertdict command
ukbb2csv/convertpheno command
ukbb2csv/convertsample command
ukbb2csv/downloader command
ukbb2csv/manifester command
ukbb2csv/manifetcher command
ukbb2disease command
ukbb2recur command
vcf2bigquery command
xml2ecg command
compileinfoprint is imported for the side effect of printing the compileinfo to os.StdErr
 compileinfoprint is imported for the side effect of printing the compileinfo to os.StdErr
example
bim command
bulkprocess
ukbb2csv
convertpheno

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