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bioinfo.pipeline.block.SeqSplit

Bioinformatics pipeline block to split sequences into separate files

Since R2023a

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  • seqsplit block icon

Description

A SeqSplit block enables you to split sequences according to the provided barcodes and save the sequences in separate files.

Creation

Syntax

b = bioinfo.pipeline.block.SeqSplit
b = bioinfo.pipeline.block.SeqSplit(options)
b = bioinfo.pipeline.block.SeqSplit(Name=Value)

Description

b = bioinfo.pipeline.block.SeqSplit creates a SeqSplit block.

example

b = bioinfo.pipeline.block.SeqSplit(options) also specifies additional options.

b = bioinfo.pipeline.block.SeqSplit(Name=Value) specifies additional options as the property names and values of a SeqSplitOptions object. This object is set as the value of the Options property of the block.

Input Arguments

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SeqSplit options, specified as a SeqSplitOptions object. The default is a default SeqSplitOptions object.

Name-Value Arguments

Specify optional pairs of arguments as Name1=Value1,...,NameN=ValueN, where Name is the argument name and Value is the corresponding value. Name-value arguments must appear after other arguments, but the order of the pairs does not matter.

Note

The following list of arguments is a partial list. For the complete list, refer to the properties of SeqSplitOptions object.

Maximum number of mismatches allowed during barcode matching, specified as a nonnegative integer. The default is 0, that is, no mismatches are allowed.

Type of barcode to match, specified as 3 or 5. A value of 5 corresponds to the barcode located at the 5' end of each sequence, and 3 corresponds to the 3' end.

Example:

Properties

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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:

    FieldDescription
    identifierIdentifier of the error that occurred
    messageText of the error message
    indexLinear 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

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.

The SeqSplit block Inputs structure has the following fields:

  • FASTQFiles — Names of FASTQ-formatted files with sequence and quality information. This input is a required input that must be satisfied.

  • BarcodeFile — Name of barcode file with barcode information. This input is a required input that must be satisfied.

The default value for each input field is a bioinfo.pipeline.datatypes.Unset object, which means that the input value is not set yet.

Data Types: struct

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 SeqSplit block Outputs structure has the following fields:

  • SplitFASTQFiles — Output file names. By default, the name of each output file consists of the input file name followed by the output suffix ('_split') and the barcode identifier.

    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.

  • NumSplit — Numbers of sequences saved in each output file, returned as a scalar or an n-by-1 vector, where n is the number of output files. If there are multiple output files, the order within n corresponds to the order of the output files.

Data Types: struct

SeqSplit options, specified as a SeqSplitOptions object. The default value is a default SeqSplitOptions object.

Object Functions

compilePerform block-specific additional checks and validations
copyCopy array of handle objects
emptyInputsCreate input structure for use with run method
evalEvaluate block object
runRun block object

Examples

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Use a SeqSplit block to split sequences into separate files based on barcodes.

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

%% 
% Create a tab-delimited file with barcode info.
barcodeInfo = {'ID1','AAAAC';'ID2', 'AGATT';'ID3', 'GACTT'};
writetable(cell2table(barcodeInfo), 'barcodeExample.txt', ...
           'Delimiter','\t','WriteVariableNames',false);
%%
%  Create and add blocks to a pipeline.
FC1 = FileChooser(which("SRR005164_1_50.fastq"));
FC2 = FileChooser(which("barcodeExample.txt"));
SS = SeqSplit;
P = Pipeline;
addBlock(P,[FC1,FC2,SS]);
connect(P,FC1,SS,["Files","FASTQFiles"]);
connect(P,FC2,SS,["Files","BarcodeFile"]);

%%
% Run the pipeline and get the results.
run(P);
R = results(P,SS)
R = 

  struct with fields:

    SplitFASTQFiles: [3×1 bioinfo.pipeline.datatypes.File]
           NumSplit: [3×1 double]

Call unwrap on SplitFASTQFiles to see the location of the generated files.

unwrap(R.SplitFASTQFiles)
ans = 

  3×1 string array

    "C:\PipelineResults\SeqSplit_1\1\SRR005164_1_50_split_ID1.fastq"
    "C:\PipelineResults\SeqSplit_1\1\SRR005164_1_50_split_ID2.fastq"
    "C:\PipelineResults\SeqSplit_1\1\SRR005164_1_50_split_ID3.fastq"

Version History

Introduced in R2023a

See Also

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