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bioinfo.pipeline.library.Library

Collection of blocks to use in bioinformatics pipelines

Since R2023b

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Description

The bioinfo.pipeline.library.Library object allows you to store configured and custom pipeline blocks for use in bioinformatics pipelines. For more information, see Bioinformatics Pipeline Block Libraries.

Creation

Use bioinfo.pipeline.library.Library to create a Library object.

Properties

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Block library name, specified as a character vector or string scalar. The library name must be a valid variable name.

Data Types: char | string

Block library description, specified as a character vector or string scalar. Use this property to add more information about the library.

Data Types: char | string

This property is read-only.

Names of blocks in the library, specified as a string scalar or string vector.

You can define the block names when you add the blocks using addBlock.

Data Types: string

This property is read-only.

Blocks in the library, specified as a bioinfo.pipeline.Block or vector of block objects.

Object Functions

addBlockAdd block to library
findBlockFind blocks from block library
removeBlockRemove blocks from block library
renameBlockRename block in block library

Examples

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Open Live Script

Import the pipeline, block, and library objects needed for the example.

import bioinfo.pipeline.library.*
import bioinfo.pipeline.block.*
import bioinfo.pipeline.Pipeline

Create a pipeline.

P = Pipeline;

Create a FileChooser block for a FASTQ file, that is provided with the toolbox, and add to the pipeline.

fastqfile = FileChooser(which("SRR005164_1_50.fastq"));
addBlock(P,fastqfile);

Create a block library directly from the pipeline.

mylib = Library(P,Name="mylib")
mylib = 
  Library with properties:

           Name: "mylib"
    Description: ""
     BlockNames: "FileChooser_1"
         Blocks: [1x1 bioinfo.pipeline.block.FileChooser]

Add a block to the library.

sequencefilter = SeqFilter(Method="MinLength");
addBlock(mylib,sequencefilter,"MinLengthSeqFilter");

Remove a block from the library.

removeBlock(mylib,"MinLengthSeqFilter");

Add a library to the list of available libraries.

addLibrary(mylib);

You can also save a library as a MAT-file and share with others. saveLibrary creates the corresponding MAT-file in the current folder. The MAT-file has the same base name as the library being saved. You may set Overwrite=true to overwrite any existing library with the same name. For instance, the following call creates mylib.mat in the current folder.

saveLibrary(mylib,Overwrite=true);

Instead of saving the file in the current directory, you can also specify an alternative location to save the file.

saveLibrary(mylib,"C:\Examples\BlockLibraries\");

Load the library from the MAT-file.

mylib2 = loadLibrary("mylib.mat");

Create a new SeqFilter block that filters sequences using their average base qualities instead. Add the block to mylib2 and rename the library.

mqseqfilter = SeqFilter(Method="MeanQuality");
addBlock(mylib,mqseqfilter,"MeanQuality");
mylib2.Name = "mylib2"
mylib2 = 
  Library with properties:

           Name: "mylib2"
    Description: ""
     BlockNames: "FileChooser_1"
         Blocks: [1x1 bioinfo.pipeline.block.FileChooser]

Add mylib2 to the list of available libraries.

addLibrary(mylib2,Overwrite=true);

Get a list of all the available libraries.

availableLibs = getLibrary
availableLibs=1×2 Library array with properties:
    Name
    Description
    BlockNames
    Blocks

Remove the library mylib from the list.

removeLibrary("mylib");
availableLibs = getLibrary
availableLibs = 
  Library with properties:

           Name: "mylib2"
    Description: ""
     BlockNames: "FileChooser_1"
         Blocks: [1x1 bioinfo.pipeline.block.FileChooser]

Version History

Introduced in R2023b

See Also

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