inputNames
Description
Examples
Connect Blocks in Bioinformatics Pipeline
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;
Add blocks to the pipeline. Optionally, you can specify the block names.
addBlock(qcpipeline,[fastqfile,sequencefilter],["FF","SF"]);
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. The output is a 1-by-2 string array, indicating the names of two ports that are now connected. You can use either the block objects themselves or the block names that you have defined previously. The next command uses the block names to identify and connect these two blocks.
connectedports = connect(qcpipeline,"FF","SF",["Files","FASTQFiles"])
connectedports = 1×2 string
"Files" "FASTQFiles"
You can also query the names of connected ports using portMap
.
portnames = portMap(qcpipeline,"FF","SF")
portnames = 1×2 string
"Files" "FASTQFiles"
Run Bioinformatics Pipeline Using Input Structure
Import the Pipeline and block objects needed for the example.
import bioinfo.pipeline.Pipeline import bioinfo.pipeline.block.*
Create a pipeline.
P = Pipeline;
Create a Bowtie2Build
block to build index files for the reference genome.
bowtie2build = Bowtie2Build;
Create a Bowtie2
block to map the read sequences to the reference sequence.
bowtie2 = Bowtie2;
Add the blocks to the pipeline.
addBlock(P,[bowtie2build,bowtie2],["bowtie2build","bowtie2"]);
Get the list of names of all the required input ports from every block in the pipeline that are needed to be set or connected. IndexBaseName
is an input port of both bowtie2build
and bowtie2
block. Reads1File
is the input port of the bowtie2
block and ReferenceFASTAFile
is the input of bowtie2build
block.
portnames = inputNames(P)
portnames = 1×3 string
"IndexBaseName" "Reads1Files" "ReferenceFASTAFiles"
Some blocks have optional input ports. To see the names of these ports, set IncludeOptional=true
. For instance, the Bowtie2
block has an optional input port (Reads2Files
) that accepts files for the second mate reads when you have paired-end read data.
allportnames = inputNames(P,IncludeOptional=true)
allportnames = 1×4 string
"IndexBaseName" "Reads1Files" "Reads2Files" "ReferenceFASTAFiles"
Create an input structure to set the input port values of the bowtie2
and bowtie2build
blocks. Specifically, set IndexBaseName
to "Dmel_chr4"
which is the base name for the reference index files for the Drosophila genome. Set Reads1Files
to "SRR6008575_10k_1.fq"
and Reads2Files
to "SRR6008575_10k_2.fq"
. Set ReferenceFASTAFile
to "Dmel_chr4.fa
". These read files are already provided with the toolbox.
inputStruct.IndexBaseName = "Dmel_chr4"; inputStruct.Reads1Files = "SRR6008575_10k_1.fq"; inputStruct.Reads2Files = "SRR6008575_10k_2.fq"; inputStruct.ReferenceFASTAFiles = "Dmel_chr4.fa";
Optionally, you can compile and check if the input structure is set up correctly. Note that this compilation also happens automatically when you run the pipeline.
compile(P,inputStruct);
Run the pipeline using the structure as an input.
run(P,inputStruct);
Get the bowtie2
block result after the pipeline finishes running.
wait(P); mappedFile = results(P,bowtie2)
mappedFile = struct with fields:
SAMFile: [1×1 bioinfo.pipeline.datatype.File]
The Bowtie2
block generates a SAM file that contains the mapped results. To see the location of the file, use unwrap
.
unwrap(mappedFile.SAMFile)
Input Arguments
pipeline
— Bioinformatics pipeline
bioinfo.pipeline.Pipeline
object
Bioinformatics pipeline, specified as a bioinfo.pipeline.Pipeline
object.
tf
— Flag to include optional input port names
false
or 0 (default) | true
or 1
Flag to include optional input port names, specified as a numeric or logical 1 (true
) or 0 (false
). An optional inport port is an input port (bioinfo.pipeline.Input
) with its Required
property set to false
.
Output Arguments
names
— Names of unconnected block inputs
string scalar | string vector
Names of unconnected block inputs, returned as a string scalar or string vector. You
can use these names as fields of the input structure in the run call
run(pipeline,inputStruct)
.
Version History
Introduced in R2023a
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