bioinfo.pipeline.block.Bowtie2Build

Bioinformatics pipeline block to create Bowtie2 index from reference sequence

Since R2023a

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Description

A Bowtie2Build block enables you to create index files from a reference sequence.

The block requires the Bowtie 2 Support Package for Bioinformatics Toolbox™. If this support package is not installed, then a download link is provided. For details, see Bioinformatics Toolbox Software Support Packages.

Creation

Syntax

b = bioinfo.pipeline.block.Bowtie2Build

b = bioinfo.pipeline.block.Bowtie2Build(options)

b = bioinfo.pipeline.block.Bowtie2Build(Name=Value)

Description

b = bioinfo.pipeline.block.Bowtie2Build creates a Bowtie2Build block.

b = bioinfo.pipeline.block.Bowtie2Build(options) also specifies additional options.

b = bioinfo.pipeline.block.Bowtie2Build(Name=Value) specifies additional options as the property names and values of a Bowtie2BuildOptions object. This object is set as the value of the Options property of the block. For example, bt2buildBlock = bioinfo.pipeline.block.Bowtie2Build(ForceLargeIndex=true) sets the ForceLargeIndex property of the object to force the creation of a large index even if the reference is less than 4 billion nucleotides long.

Input Arguments

options — Bowtie2Build options

Bowtie2BuildOptions | string | character vector

Bowtie2Build options, specified as a Bowtie2BuildOptions object, string, or character vector.

If you are specifying a string or character vector, it must be in the native bowtie2 option syntax (prefixed by one or two dashes) [1].

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 Bowtie2BuildOptions object.

BuildOnlyReference — Boolean indicator to build only bitpacked reference

false (default) | true

Boolean indicator to build only the 3.bt2 and 4.bt2 files that correspond to the bitpacked version of reference sequences, specified as true or false.

Data Types: logical

BuildNoReference — Boolean indicator to omit building bitpacked reference

false (default) | true

Boolean indicator to omit building the 3.bt2 and 4.bt2 files that correspond to the bitpacked version of reference sequences, specified as true or false.

Data Types: logical

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 Bowtie2Build block Inputs structure has the following fields:

• ReferenceFASTAFiles — Names of files with reference sequence information. This input is a required input that must be satisfied.

• IndexBaseName — Base name of the reference index files. The index files are in the BT2 or BT21 format. For example, if you specify "Dmel_chr4" as IndexBaseName, the generated index files would be Dmel_chr4.1.bt2, Dmel_chr4.2.bt2, and so on. This input is optional, and by default, the block uses "Bowtie2Index" as the prefix.

The default value for each of these inputs 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 Bowtie2Build block Outputs structure has the field named IndexBaseName.

Data Types: struct

Options — Bowtie2Build options

Bowtie2BuildOptions object (default)

Bowtie2Build options, specified as a Bowtie2BuildOptions object. The default value is a default Bowtie2BuildOptions 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

Fetch Parallel-Running Block Results from Bioinformatics Pipeline

Import the pipeline and block objects needed for the example.

import bioinfo.pipeline.Pipeline
import bioinfo.pipeline.blocks.*

Create a pipeline.

P = Pipeline;

A FileChooser block can take in a URL of a remote file as an input and download the file to make it available for the downstream blocks. Download the file Homo_sapiens.GRCh38.dna.chromosome.19.fa.gz that contains the human reference genome chromosome 19 in the FASTA format.

chr19url = "http://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.19.fa.gz";
fileChooserBlock1 = FileChooser(chr19url);

A UserFunction block to unzip the downloaded reference genome file using the gunzip function. When you create the block, you can specify the function to call and set the input and output port names that map to the input and output arguments of the corresponding function, respectively. In this example, name the input port as "ZippedFilenames" and the output port as "UnzippedFilenames"

gunzipUserFunctionBlock = UserFunction(@gunzip,RequiredArguments="ZippedFilenames",OutputArguments="UnzippedFilenames");

The reference genome file needs to be indexed in before reads can be aligned to it. To generate the indices, create a Bowtie2Build block.

bowtie2BuildBlock = Bowtie2Build;

Add the blocks.

addBlock(P,[fileChooserBlock1,gunzipUserFunctionBlock,bowtie2BuildBlock]);

Connect the output port named "Files" of fileChooserBlock1 to the input port named "ZippedFileNames" of gunzipUserFunctionBlock. Also connect the output "UnzippedFilenames" of gunzipUserFunctionBlock to the input "ReferenceFASTAFiles" of bowtie2BuildBlock.

connect(P,fileChooserBlock1,gunzipUserFunctionBlock,["Files","ZippedFilenames"]);
connect(P,gunzipUserFunctionBlock,bowtie2BuildBlock,["UnzippedFilenames","ReferenceFASTAFiles"]);

Create blocks for downloading RNA-seq data.

adrenal_1_url = "https://usegalaxy.org/dataset/display?dataset_id=d44d2a324474d1aa&to_ext=fq";
adrenal_2_url = "https://usegalaxy.org/dataset/display?dataset_id=d08360a1c0ffdc62&to_ext=fq";
brain_1_url =   "https://usegalaxy.org/dataset/display?dataset_id=f187acb8015d6c7f&to_ext=fq";
brain_2_url =   "https://usegalaxy.org/dataset/display?dataset_id=08c45996966d7ded&to_ext=fq";
fileChooserBlock2 = FileChooser([brain_1_url;adrenal_1_url]);
fileChooserBlock3 = FileChooser([brain_2_url;adrenal_2_url]);

Create a Bowtie2 block for mapping reads.

bowtie2Block = Bowtie2;

Add blocks to the pipeline.

addBlock(P,[fileChooserBlock2,fileChooserBlock3,bowtie2Block]);

Connect the blocks.

connect(P,bowtie2BuildBlock,bowtie2Block,["IndexBaseName","IndexBaseName"]);
connect(P,fileChooserBlock2,bowtie2Block,["Files","Reads1Files"]);
connect(P,fileChooserBlock3,bowtie2Block,["Files","Reads2Files"]);

Run the pipeline in parallel.

run(P,UseParallel=true);

Starting parallel pool (parpool) using the 'Processes' profile ...
Connected to parallel pool with 4 workers.

If you try to get the block results while the pipeline is still running, you get an incomplete result.

bt2Results = results(P,bowtie2Block)

bt2Results = 
  Incomplete pipeline result.

Use fetchResults to wait for the blocks that are running in parallel to complete and get the results.

bt2Results = fetchResults(P,bowtie2Block)

bt2Results = struct with fields:
    SAMFile: [1×1 bioinfo.pipeline.datatype.File]

Tip: Use the unwrap method to see the location of the output file. For example, unwrap(bt2Results.SAMFile) shows the location of the sorted SAM file.

Alternatively, you can use the following two commands instead of fetchResults.

wait(P,bowtie2Block);
bt2Results = results(P,bowtie2Block);

References

[1] Langmead, B., and S. Salzberg. "Fast gapped-read alignment with Bowtie 2." Nature Methods. 9, 2012, 357–359.

Version History

Introduced in R2023a