bioinfo.pipeline.library.getLibrary

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]