processTable
Description
Examples
Check Bioinformatics Pipeline Run Status and Results
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 FileChooser
block that takes in a SAM file as an input.
samFile = FileChooser(which("Myco_1_1.sam"));
Create a SeqTrim
block.
trimsequences = SeqTrim;
Add blocks to the pipeline.
addBlock(P,[samFile,trimsequences]);
Check the names of the output port and input port of the blocks to connect.
samFile.Outputs
ans = struct with fields:
Files: [1x1 bioinfo.pipeline.Output]
trimsequences.Inputs
ans = struct with fields:
FASTQFiles: [1x1 bioinfo.pipeline.Input]
Connect the ports.
connect(P,samFile,trimsequences,["Files","FASTQFiles"]);
The block returns an incomplete result as the block has not yet run.
results(P,trimsequences)
ans = Incomplete result (0x0) with the following outputs: TrimmedFASTQFiles NumTrimmed NumUntrimmed Not Run: 0 Complete: 0 Error: 0
Run the pipeline and check the run status of each block in the process table. The samFile
block had no error, but the SeqTrim
block generated an error as indicated by the Status
column. The SeqTrim
block generated an error because it was expecting a FASTQ file as an input but received a SAM file instead.
run(P); t = processTable(P,Expanded=true)
t=2×5 table
Block Status RunStart RunEnd RunErrors
_______________ _________ ____________________ ____________________ ________________
"FileChooser_1" Completed 20-Jul-2024 18:14:57 20-Jul-2024 18:14:57 {0x0 MException}
"SeqTrim_1" Error 20-Jul-2024 18:14:58 20-Jul-2024 18:14:58 {1x1 MException}
You can see the printed error message at the MATLAB® command line. You can also enter the following commands to see the message.
seqTrimInfo = t(2,:); seqTrimInfo.RunErrors{:}
Input Arguments
pipeline
— Bioinformatics pipeline
bioinfo.pipeline.Pipeline
object
Bioinformatics pipeline, specified as a bioinfo.pipeline.Pipeline
object.
blocks
— Pipeline blocks
bioinfo.pipeline.Block
object | vector of objects | character vector | string scalar | ...
Pipeline blocks, specified as a bioinfo.pipeline.Block
object, vector of block objects, character vector,
string scalar, string vector, or cell array of character vectors representing block
names.
tf
— Flag to contain one row per each independent block run
false
or 0 (default) | true
or 1
Flag to contain one row per each independent block run or group all runs of the same
block into a single row, specified as a numeric or logical 1 (true
)
or 0 (false
).
Each row in the table represents a block, and there are corresponding Status, RunStart, RunEnd, and RunErrors columns for each block.
By default, the function groups (or collapses) all runs of the same block into a
single row. If a block is run n independent times (per its
SplitDimension
property of the input port), then the table
variable value for each column is an n-by-1 cell array. For instance,
the next figure is an example of a (default) collapsed process table (Expanded
= false
). Note that for the Bowtie2_1,
SamSort_1 and Cufflinks_1 blocks, the table
variable values are 2-by-1 cell arrays because each of these blocks were run 2 times
independently.
The next figure is the same table with the expanded cell array (Expanded =
true
).
Output Arguments
t
— Table containing information on pipeline processes
table
Table containing information on pipeline processes, returned as a table.
Each row in the table represents a block, and there are corresponding Status, RunStart, RunEnd, and RunErrors columns for each block.
Version History
Introduced in R2023a
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