Package ubic.gemma.core.datastructure.matrix.io

Class MexMatrixWriter

java.lang.Object

ubic.gemma.core.datastructure.matrix.io.MexMatrixWriter

All Implemented Interfaces:

ExpressionDataMatrixWriter<SingleCellExpressionDataMatrix<?>,SingleCellExpressionDataVector>, SingleCellExpressionDataMatrixWriter

public class MexMatrixWriter
extends Object
implements SingleCellExpressionDataMatrixWriter

Writes SingleCellExpressionDataMatrix to the 10x MEX format.

The data is written as a TAR archive containing the following entries for each bioassay: {bioAssayName}/barcodes.tsv, {bioAssayName}/features.tsv, {bioAssayName}/matrix.mtx. If using the directory output, individual files are compressed and will have a .gz extension.

Author:

poirigui

Constructor Summary

Constructors

Constructor	Description
MexMatrixWriter()

Method Summary

Modifier and Type	Method	Description
void	setAutoFlush(boolean autoFlush)	Flush every time a complete line is written.
void	setExecutorService(Executor executorService)	Executor to use to write MEX files in parallel.
void	setScaleType(ScaleType scaleType)	Set the scale type to use when writing the matrix.
void	setUseEnsemblIds(boolean useEnsemblIds)	Use Ensembl gene IDs instead of gene symbols.
int	write(Stream<SingleCellExpressionDataVector> vectors, int numVecs, Map<BioAssay,Long> nnzBySample, Map<CompositeSequence,Set<Gene>> cs2gene, Path outputDir)	Writes a stream of vectors to a directory.
int	write(SingleCellExpressionDataMatrix<?> matrix, Class<? extends SingleCellExpressionDataVector> vectorType, OutputStream stream)	Write the matrix to the given output stream.
int	write(SingleCellExpressionDataMatrix<?> matrix, Class<? extends SingleCellExpressionDataVector> vectorType, Writer stream)	Write the matrix to the given writer.
int	write(SingleCellExpressionDataMatrix<?> matrix, Map<CompositeSequence,Set<Gene>> cs2gene, OutputStream stream)	Write a MEX matrix as a TAR archive to the given output stream.
int	write(SingleCellExpressionDataMatrix<?> matrix, Map<CompositeSequence,Set<Gene>> cs2gene, Path outputDir)	Write a matrix to a directory.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface ubic.gemma.core.datastructure.matrix.io.SingleCellExpressionDataMatrixWriter

write, write

Constructor Details

MexMatrixWriter

public MexMatrixWriter()

Method Details

write

public int write(SingleCellExpressionDataMatrix<?> matrix,
 Class<? extends SingleCellExpressionDataVector> vectorType,
 Writer stream)
          throws IOException

Description copied from interface: ExpressionDataMatrixWriter

Write the matrix to the given writer.

Specified by:

write in interface ExpressionDataMatrixWriter<SingleCellExpressionDataMatrix<?>,SingleCellExpressionDataVector>

Parameters:

vectorType - the type of vectors to write. This helps the writer determine how the QuantitationType of the matrix should be interpreted.

Returns:

the number of vectors written

Throws:

IOException

write

public int write(SingleCellExpressionDataMatrix<?> matrix,
 Class<? extends SingleCellExpressionDataVector> vectorType,
 OutputStream stream)
          throws IOException

Description copied from interface: ExpressionDataMatrixWriter

Write the matrix to the given output stream.

Specified by:

write in interface ExpressionDataMatrixWriter<SingleCellExpressionDataMatrix<?>,SingleCellExpressionDataVector>

Returns:

the number of vectors written

Throws:

IOException

write

public int write(SingleCellExpressionDataMatrix<?> matrix,
 @Nullable
 Map<CompositeSequence,Set<Gene>> cs2gene,
 OutputStream stream)
          throws IOException

Write a MEX matrix as a TAR archive to the given output stream.

Throws:

IOException

write

public int write(SingleCellExpressionDataMatrix<?> matrix,
 @Nullable
 Map<CompositeSequence,Set<Gene>> cs2gene,
 Path outputDir)
          throws IOException

Write a matrix to a directory.

Throws:

IOException

write

public int write(Stream<SingleCellExpressionDataVector> vectors,
 int numVecs,
 Map<BioAssay,Long> nnzBySample,
 @Nullable
 Map<CompositeSequence,Set<Gene>> cs2gene,
 Path outputDir)
          throws IOException

Writes a stream of vectors to a directory.

Parameters:

vectors - a stream of vectors

numVecs - the total number of vectors to write

nnzBySample - the number of non-zeroes by sample

cs2gene - a mapping of design elements to their corresponding gene(s)

Throws:

IOException

setAutoFlush

public void setAutoFlush(boolean autoFlush)

Description copied from interface: ExpressionDataMatrixWriter

Flush every time a complete line is written.

This is not very efficient, but it can be used to view the output of a matrix as it is being written.

Specified by:

setAutoFlush in interface ExpressionDataMatrixWriter<SingleCellExpressionDataMatrix<?>,SingleCellExpressionDataVector>

setScaleType

public void setScaleType(@Nullable
 ScaleType scaleType)

Description copied from interface: ExpressionDataMatrixWriter

Set the scale type to use when writing the matrix.

When null, the original values must be used.

Specified by:

setScaleType in interface ExpressionDataMatrixWriter<SingleCellExpressionDataMatrix<?>,SingleCellExpressionDataVector>

setUseEnsemblIds

public void setUseEnsemblIds(boolean useEnsemblIds)

Use Ensembl gene IDs instead of gene symbols.

setExecutorService

public void setExecutorService(Executor executorService)

Executor to use to write MEX files in parallel.