Main Content

bioinfo.pipeline.library.addLibrary

Add block library

Since R2023b

Description

example

bioinfo.pipeline.library.addLibrary(lib) adds the block library lib to the list of available libraries. For more information, see Bioinformatics Pipeline Block Libraries.

example

bioinfo.pipeline.library.addLibrary(lib,Overwrite=tf) specifies whether to overwrite an existing library with the same name.

Examples

collapse all

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]

Input Arguments

collapse all

Block library, specified as a bioinfo.pipeline.library.Library object.

Flag to overwrite an existing library with the same name, specified as a numeric or logical 1 (true) or 0 (false). By default, the function does not overwrite the existing library.

Data Types: double | logical

Version History

Introduced in R2023b