bioinfo.pipeline.block.SamSort

Bioinformatics pipeline block to sort SAM files

Since R2023a

• 

Description

A SamSort block enables you to sort alignment records from SAM files by the reference sequence name first, and then by position within the reference.

Creation

Syntax

fcBlock = bioinfo.pipeline.block.SamSort

fcBlock = bioinfo.pipeline.block.SamSort(outFileName)

Description

fcBlock = bioinfo.pipeline.block.SamSort creates a SamSort block.

fcBlock = bioinfo.pipeline.block.SamSort(outFileName) specifies the output file name.

Input Arguments

outFileName — Name of output file

string | character vector

Name of the output file, specified as a string or character vector. The file extension must be .sam.

Data Types: char | string

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 SamSort block Inputs structure has the following field:

• SAMFile — Name of a SAM file. 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 SamSort block Outputs structure has the following field:

• SortedSAMFile — Output file name. By default, it has the same base name as the input SAM file but with the extension .sorted.sam.

  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.

Data Types: struct

OutFilename — Output file name

string

Output file name, specified as a string. If it is empty, the output file will have the same base name as the input file with the extension .sorted.sam.

Data Types: 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

Sort SAM File Using SamSort Block

Sort a sample SAM file using a SamSort block.

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

FC = FileChooser(which("Myco_1_1.sam"));
SS = SamSort;
P = Pipeline;

addBlock(P,[FC,SS]);
connect(P,FC,SS,["Files","SAMFile"]);

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

R = 

  struct with fields:

    SortedSAMFile: [1×1 bioinfo.pipeline.datatypes.File]

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

unwrap(R.SortedSAMFile)

ans = 

    "C:\PipelineResults\SamSort_1\1\Myco_1_1.sorted.sam"

Version History

Introduced in R2023a