bioinfo.pipeline.block.SeqTrim

Bioinformatics pipeline block to trim sequences

Since R2023a

• 

Description

A SeqTrim block enables you to trim sequences based on a specified criterion.

Creation

Syntax

b = bioinfo.pipeline.block.SeqTrim

b = bioinfo.pipeline.block.SeqTrim(options)

b = bioinfo.pipeline.block.SeqTrim(Name=Value)

Description

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

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

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

Note

The block always overwrites existing output files, unlike the seqtrim function.

Input Arguments

options — SeqTrim options

bioinfo.pipeline.options.SeqTrimOptions

SeqTrim options, specified as a SeqTrimOptions object.

Data Types: char | string

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 SeqTrimOptions object.

Encoding — Base quality encoding format

'Illumina18' (default) | 'Sanger' | 'Solexa' | 'Illumina13' | 'Illumina15'

Base quality encoding format, specified as a character vector or string.

Method — Criterion to trim sequences

'MaxNumberLowQualityBases' (default) | 'MaxPercentLowQualityBases' | 'MeanQuality' | 'BasePositions' | 'Termini'

Criterion to trim sequences, specified as one of the following options. Specify only one trimming criterion per function call.

• 'MaxNumberLowQualityBases'– applies a maximum threshold on the number of low-quality bases allowed before trimming a sequence starting at the 5' end.

• 'MaxPercentLowQualityBases'– applies a maximum threshold on the percentage of low-quality bases allowed before trimming a sequence starting at the 5' end.

• 'MeanQuality'– applies a minimum threshold on the running average base quality allowed before trimming a sequence starting at the 5' end.

• 'BasePositions'– trims each sequence according to the base positions (first base and last base) starting at the 5' end.

• 'Termini'– trims each sequence from either the 5' or 3' end or from both ends.

Use this name-value pair argument together with 'Threshold' to specify the appropriate threshold value. Depending on the trimming criterion, the corresponding value for 'Threshold' varies. See the 'Threshold' option for the default values.

Note

Sequences resulting in empty sequences after trimming are saved in the output files as empty sequences. To remove empty sequences from files, use the seqfilter function with the 'MinLength' option set to the value of 1.

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

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.

The SeqTrim block Inputs structure has the following field:

• FASTQFiles — Names of FASTQ-formatted files with sequence and quality information. This input is a required input that must be satisfied. The default value is a bioinfo.pipeline.datatypes.Unset object, which means that the input value is not set yet.

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 SeqTrim block Outputs structure has the following fields:

• TrimmedFASTQFiles — Output file names. By default, the name of each output file consists of the input file name followed by the output suffix ('_trimmed').

  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.

• NumTrimmed — Number of sequences trimmed from each input file, returned as a scalar or an n-by-1 vector where n is the number of input files. If there are multiple input files, the order in NumTrimmed corresponds to the order of the input files.

• NumUntrimmed — Number of sequences untrimmed from each input file, returned as a scalar or an n-by-1 vector where n is the number of input files. If there are multiple input files, the order in NumUntrimmed corresponds to the order of the input files.

Data Types: struct

Options — SeqTrim options

bioinfo.pipeline.options.SeqTrimOptions object (default)

SeqTrim options, specified as a SeqTrimOptions object. The default value is a default SeqTrimOptions object.

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

Trim Sequences Using SeqTrim Block

Use a SeqTrim block to start scanning the sequence at the 5' end and trim at the first base with a low quality score of 10 (default).

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

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

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

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

R = 

  struct with fields:

    TrimmedFASTQFiles: [1×1 bioinfo.pipeline.datatypes.File]
           NumTrimmed: 1495
         NumUntrimmed: 8505

Call unwrap on TrimmedFASTQFiles to see the location of the output file.

unwrap(R.TrimmedFASTQFiles)

ans = 

    "C:\PipelineResults\SeqTrim_1\1\SRR6008575_10k_1_trimmed.fastq"

Version History

Introduced in R2023a