bioinfo.pipeline.block.FileChooser

Bioinformatics pipeline block to select files or URLs

Since R2023a

• 

Description

A FileChooser block enables you to select files or download files from URLs.

Creation

Syntax

fcBlock = bioinfo.pipeline.block.FileChooser

fcBlock = bioinfo.pipeline.block.FileChooser(fileNames)

Description

fcBlock = bioinfo.pipeline.block.FileChooser creates a FileChooser block.

fcBlock = bioinfo.pipeline.block.FileChooser(fileNames) also sets the Files property of the block to fileNames.

Input Arguments

fileNames — Names of files or URLs

string | character vector | ...

Names of files or URLs, specified as a string, character vector, string vector, or cell array of character vectors. You can include a full file path. The block does not use the MATLAB^® path.

Data Types: char | string | cell

Properties

ErrorHandler — Function to handle errors from run method

function handle

Function to handle errors from the run method of the block, specified as a function handle. The handle specifies the function to call if the run method encounters an error within a pipeline. For the pipeline to continue after a block fails, ErrorHandler must return a structure that is compatible with the output ports of the block. The error handling function is called with the following two inputs:

• Structure with these fields:

  Field	Description
  identifier	Identifier of the error that occurred
  message	Text of the error message
  index	Linear index indicating which block process failed in the parallel run. By default, the index is 1 because there is only one run per block. For details on how block inputs can be split across different dimensions for multiple run calls, see Bioinformatics Pipeline SplitDimension.

• Input structure passed to the run method when it fails

Data Types: function_handle

Files — File names or URLs

empty string array (default) | string | character vector | ...

Names of files or URLs, specified as a string, character vector, string vector, or cell array of character vectors.

Files is always appended after PathRoot to determine the file or URL destinations. Files can include file, http, https as a scheme if PathRoot is empty.

Data Types: char | string | cell

Inputs — Input ports

structure

This property is read-only.

Input ports of the block, specified as a structure. The field names of the structure are the names of the block input ports, and the field values are bioinfo.pipeline.Input objects. These objects describe the input port behaviors. The input port names are the expected field names of the input structure that you pass to the block run method.

Data Types: struct

Outputs — Output ports

structure

This property is read-only.

Output ports of the block, specified as a structure. The field names of the structure are the names of the block output ports, and the field values are bioinfo.pipeline.Output objects. These objects describe the output port behaviors. The field names of the output structure returned by the block run method are the same as the output port names.

The FileChooser block Outputs structure has the following field:

• Files — Output file names.

  .

  Tip

  To see the actual location of these files, first get the results of the block. Then use the unwrap method as shown in this example.

Data Types: struct

Options — Parameters for obtaining data from web server

weboptions object (default)

Parameters for obtaining data from a web server, specified as a weboptions object.

This property is used only when the scheme is http or https, or when Files contains a URL. The default value is a weboptions object with default property values.

PathRoot — Root path for Files

empty string array (default) | string | character vector

Root path for all files in the Files property, specified as a string or character vector.

PathRoot is always prefixed to Files to determine the file or URL destinations.

Data Types: char | string

Object Functions

compile	Perform block-specific additional checks and validations
copy	Copy array of handle objects
emptyInputs	Create input structure for use with run method
eval	Evaluate block object
run	Run block object

Examples

Create a Simple Pipeline to Plot Sequence Quality Data

Import the Pipeline and block objects needed for the example.

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

Create a pipeline.

qcpipeline = Pipeline;

Select an input FASTQ file using a FileChooser block.

fastqfile = FileChooser(which("SRR005164_1_50.fastq"));

Create a SeqFilter block.

sequencefilter = SeqFilter;

Define the filtering threshold value. Specifically, filter out sequences with a total of more than 10 low-quality bases, where a base is considered a low-quality base if its quality score is less than 20.

sequencefilter.Options.Threshold = [10 20];

Add the blocks to the pipeline.

addBlock(qcpipeline,[fastqfile,sequencefilter]);

Connect the output of the first block to the input of the second block. To do so, you need to first check the input and output port names of the corresponding blocks.

View the Outputs (port of the first block) and Inputs (port of the second block).

fastqfile.Outputs

ans = struct with fields:
    Files: [1×1 bioinfo.pipeline.Output]

sequencefilter.Inputs

ans = struct with fields:
    FASTQFiles: [1×1 bioinfo.pipeline.Input]

Connect the Files output port of the fastqfile block to the FASTQFiles port of sequencefilter block.

connect(qcpipeline,fastqfile,sequencefilter,["Files","FASTQFiles"]);

Next, create a UserFunction block that calls the seqqcplot function to plot the quality data of the filtered sequence data. In this case, inputFile is the required argument for the seqqcplot function. The required argument name can be anything as long as it is a valid variable name.

qcplot = UserFunction("seqqcplot",RequiredArguments="inputFile",OutputArguments="figureHandle");

Alternatively, you can also use dot notation to set up your UserFunction block.

qcplot = UserFunction;
qcplot.RequiredArguments = "inputFile";
qcplot.Function = "seqqcplot";
qcplot.OutputArguments = "figureHandle";

Add the block.

addBlock(qcpipeline,qcplot);

Check the port names of sequencefilter block and qcplot block.

sequencefilter.Outputs

ans = struct with fields:
    FilteredFASTQFiles: [1×1 bioinfo.pipeline.Output]
         NumFilteredIn: [1×1 bioinfo.pipeline.Output]
        NumFilteredOut: [1×1 bioinfo.pipeline.Output]

qcplot.Inputs

ans = struct with fields:
    inputFile: [1×1 bioinfo.pipeline.Input]

Connect the FilteredFASTQFiles port of the sequencefilter block to the inputFile port of the qcplot block.

connect(qcpipeline,sequencefilter,qcplot,["FilteredFASTQFiles","inputFile"]);

Run the pipeline to plot the sequence quality data.

run(qcpipeline);

Select Input File Using FileChooser Block

Use a FileChooser block to select an input file provided with the toolbox.

import bioinfo.pipeline.block.FileChooser
import bioinfo.pipeline.Pipeline

FC = FileChooser(which("SRR6008575_10k_1.fq"));

P = Pipeline;
addBlock(P, FC);

run(P);
R = results(P, FC)

R = 

  struct with fields:

    Files: [1×1 bioinfo.pipeline.datatypes.File]

Call unwrap on Files to see the location of the file.

unwrap(R.Files)

ans = 

    "C:\Program Files\MATLAB\R2023a\toolbox\bioinfo\bioinfodata\SRR6008575_10k_1.fq"

Version History

Introduced in R2023a