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Xprize update

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Former-commit-id: d38919a897961e4d40da3b844057c3fb94fdb6d7
This commit is contained in:
Eric Coissac
2024-07-25 18:09:03 -04:00
parent 4e4fac491f
commit 67665a6b40
18 changed files with 895 additions and 29 deletions
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37
pkg/obitools/obiconsensus/obiconsensus.go
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@@ -52,7 +52,7 @@ func BuildConsensus(seqs obiseq.BioSequenceSlice,
}
log.Printf("Number of reads : %d\n", len(seqs))
log.Debugf("Number of reads : %d\n", len(seqs))
if kmer_size < 0 {
longest := make([]int, len(seqs))
@@ -64,7 +64,7 @@ func BuildConsensus(seqs obiseq.BioSequenceSlice,
}
kmer_size = slices.Max(longest) + 1
log.Printf("estimated kmer size : %d", kmer_size)
log.Debugf("estimated kmer size : %d", kmer_size)
}
var graph *obikmer.DeBruijnGraph
@@ -80,7 +80,7 @@ func BuildConsensus(seqs obiseq.BioSequenceSlice,
}
kmer_size++
log.Infof("Cycle detected, increasing kmer size to %d\n", kmer_size)
log.Debugf("Cycle detected, increasing kmer size to %d\n", kmer_size)
}
if save_graph {
@@ -96,7 +96,7 @@ func BuildConsensus(seqs obiseq.BioSequenceSlice,
}
}
log.Printf("Graph size : %d\n", graph.Len())
log.Debugf("Graph size : %d\n", graph.Len())
total_kmer := graph.Len()
seq, err := graph.LongestConsensus(consensus_id)
@@ -260,6 +260,21 @@ func MinionDenoise(graph *obigraph.Graph[*obiseq.BioSequence, Mutation],
sample_key string, kmer_size int) obiseq.BioSequenceSlice {
denoised := obiseq.MakeBioSequenceSlice(len(*graph.Vertices))
bar := (*progressbar.ProgressBar)(nil)
if obiconvert.CLIProgressBar() {
pbopt := make([]progressbar.Option, 0, 5)
pbopt = append(pbopt,
progressbar.OptionSetWriter(os.Stderr),
progressbar.OptionSetWidth(15),
progressbar.OptionShowIts(),
progressbar.OptionSetPredictTime(true),
progressbar.OptionSetDescription(fmt.Sprintf("[Build consensus] on %s", graph.Name)),
)
bar = progressbar.NewOptions(len(*graph.Vertices), pbopt...)
}
for i, v := range *graph.Vertices {
var err error
var clean *obiseq.BioSequence
@@ -283,6 +298,7 @@ func MinionDenoise(graph *obigraph.Graph[*obiseq.BioSequence, Mutation],
clean.SetAttribute("obiconsensus_consensus", true)
}
pack.Recycle(false)
} else {
clean = obiseq.NewBioSequence(v.Id(), v.Sequence(), v.Definition())
clean.SetAttribute("obiconsensus_consensus", false)
@@ -295,7 +311,20 @@ func MinionDenoise(graph *obigraph.Graph[*obiseq.BioSequence, Mutation],
clean.SetAttribute("obiconsensus_weight", int(1))
}
annotations := v.Annotations()
for k, v := range annotations {
if !clean.HasAttribute(k) {
clean.SetAttribute(k, v)
}
}
denoised[i] = clean
if bar != nil {
bar.Add(1)
}
}
return denoised