bioinfo.pipeline.block.SeqFilter

Use a SeqFilter block to filter out sequences with low-quality bases, where a base is considered low-quality if its quality score is less than 15 (default).

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

FC = FileChooser(which("SRR005164_1_50.fastq"));
SF = SeqFilter;

P = Pipeline;
addBlock(P,[FC,SF]);
connect(P,FC,SF,["Files","FASTQFiles"]);

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

R = 

  struct with fields:

    FilteredFASTQFiles: [1×1 bioinfo.pipeline.datatypes.File]
         NumFilteredIn: 3
        NumFilteredOut: 47

unwrap(R.FilteredFASTQFiles)

ans = 

    "C:\PipelineResults\SeqFilter_1\1\SRR005164_1_50_filtered.fastq"

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);