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7a979ba77f
This commit adds the implementation of the obisuperkmer command, including: - The main command in cmd/obitools/obisuperkmer/ - The package implementation in pkg/obitools/obisuperkmer/ - Automated tests in obitests/obitools/obisuperkmer/ - Documentation for the implementation and tests The obisuperkmer command extracts super k-mers from DNA sequences, following the standard OBITools architecture. It includes proper CLI option handling, validation of parameters, and integration with the OBITools pipeline system. Tests cover basic functionality, parameter validation, output format, metadata preservation, and file I/O operations.
60 lines
2.0 KiB
Go
60 lines
2.0 KiB
Go
package obisuperkmer
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import (
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log "github.com/sirupsen/logrus"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obikmer"
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)
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// CLIExtractSuperKmers extracts super k-mers from an iterator of BioSequences.
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//
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// This function takes an iterator of BioSequence objects, extracts super k-mers
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// from each sequence using the k-mer and minimizer sizes specified by CLI options,
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// and returns a new iterator yielding the extracted super k-mers as BioSequence objects.
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//
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// Each super k-mer is a maximal subsequence where all consecutive k-mers share
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// the same minimizer. The resulting BioSequences contain metadata including:
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// - minimizer_value: the canonical minimizer value
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// - minimizer_seq: the DNA sequence of the minimizer
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// - k: the k-mer size used
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// - m: the minimizer size used
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// - start: starting position in the original sequence
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// - end: ending position in the original sequence
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// - parent_id: ID of the parent sequence
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//
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// Parameters:
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// - iterator: an iterator yielding BioSequence objects to process.
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//
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// Returns:
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// - An iterator yielding BioSequence objects representing super k-mers.
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func CLIExtractSuperKmers(iterator obiiter.IBioSequence) obiiter.IBioSequence {
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// Get k-mer and minimizer sizes from CLI options
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k := CLIKmerSize()
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m := CLIMinimizerSize()
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// Validate parameters
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if m < 1 || m >= k {
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log.Fatalf("Invalid parameters: minimizer size (%d) must be between 1 and k-1 (%d)", m, k-1)
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}
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if k < 2 || k > 31 {
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log.Fatalf("Invalid k-mer size: %d (must be between 2 and 31)", k)
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}
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log.Printf("Extracting super k-mers with k=%d, m=%d", k, m)
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// Create the worker for super k-mer extraction
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worker := obikmer.SuperKmerWorker(k, m)
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// Apply the worker to the iterator with parallel processing
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newIter := iterator.MakeIWorker(
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worker,
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false, // don't merge results
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obidefault.ParallelWorkers(),
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)
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return newIter
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}
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