Get bioinformatics pipeline results
Get Block Results from Bioinformatics Pipeline
Import the pipeline and block objects needed for the example.
import bioinfo.pipeline.Pipeline import bioinfo.pipeline.block.*
Create a pipeline.
P = Pipeline;
Create the FileChooser and SamSort blocks.
FCB = FileChooser(which("ex1.sam")); SSB = SamSort;
Add blocks to the pipeline and connect them.
Run the pipeline.
The outputs of the FileChooser and SamSort blocks are files that are saved to your file system.
fcbResults = results(P,FCB)
fcbResults = struct with fields: Files: [1×1 bioinfo.pipeline.datatype.File]
ssbResults = results(P,SSB)
ssbResults = struct with fields: SortedSAMFile: [1×1 bioinfo.pipeline.datatype.File]
Tip: Use the
unwrap method to see the location of the output file. For example,
unwrap(ssbResults.SortedSAMFiles) shows the location of the sorted SAM file.
pipeline — Bioinformatics pipeline
Bioinformatics pipeline, specified as a
blockResults — Block results
Block results, returned as a structure or
bioinfo.pipeline.datatypes.Incomplete object. The
Incomplete object is returned if the block results are not yet
computed or available.
If it is a structure, the field names are the output port names of the block, and
the field values are the output values. If you have not run the pipeline or the results
are not available yet, each output value has the default value of
Incomplete, which is a
Introduced in R2023a