obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-12-12 18:30:25 +00:00
Code Issues Packages Projects Releases Wiki Activity

Add some code refactoring from the blackboard branch

Browse Source
This commit is contained in:
Eric Coissac
2024-08-02 12:35:46 +02:00
parent bc1aaaf7d9
commit 1b1cd41fd3
38 changed files with 491 additions and 330 deletions
Download Patch File Download Diff File Expand all files Collapse all files

11
pkg/obitools/obiconsensus/obiconsensus.go
View File

@@ -46,7 +46,12 @@ func BuildConsensus(seqs obiseq.BioSequenceSlice,
if err == nil {
defer fasta.Close()
fasta.Write(obiformats.FormatFastaBatch(obiiter.MakeBioSequenceBatch(0, seqs), obiformats.FormatFastSeqJsonHeader, false))
fasta.Write(obiformats.FormatFastaBatch(obiiter.MakeBioSequenceBatch(
fmt.Sprintf("%s_consensus", consensus_id),
0,
seqs,
),
obiformats.FormatFastSeqJsonHeader, false).Bytes())
fasta.Close()
}
@@ -333,7 +338,7 @@ func CLIOBIMinion(itertator obiiter.IBioSequence) obiiter.IBioSequence {
dirname := CLIGraphFilesDirectory()
newIter := obiiter.MakeIBioSequence()
db := itertator.Load()
source, db := itertator.Load()
log.Infof("Sequence dataset of %d sequeences loaded\n", len(db))
@@ -394,7 +399,7 @@ func CLIOBIMinion(itertator obiiter.IBioSequence) obiiter.IBioSequence {
CLISampleAttribute(),
CLIKmerSize())
newIter.Push(obiiter.MakeBioSequenceBatch(sample_order, denoised))
newIter.Push(obiiter.MakeBioSequenceBatch(source, sample_order, denoised))
sample_order++
}