bioinfo.pipeline.block.FileChooser
Description
A FileChooser
block enables you to select files or download files
from URLs.
Creation
Syntax
Description
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:
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
See Also
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