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Some code refactoring, a new version of obiuniq more efficient in memory and a first make file allowing to build obitools

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This commit is contained in:
Eric Coissac
2022-02-24 07:08:40 +01:00
parent 2e7c1834b0
commit eaf65fbcce
39 changed files with 1225 additions and 241 deletions
Download Patch File Download Diff File Expand all files Collapse all files
pkg/obitools/obipairing/options.go
+4 -4
View File
@@ -1,7 +1,7 @@
package obipairing
import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"github.com/DavidGamba/go-getoptions"
)
@@ -47,15 +47,15 @@ func OptionSet(options *getoptions.GetOpt) {
PairingOptionSet(options)
}
func IBatchPairedSequence() (obiseq.IPairedBioSequenceBatch, error) {
func IBatchPairedSequence() (obiiter.IPairedBioSequenceBatch, error) {
forward, err := obiconvert.ReadBioSequencesBatch(_ForwardFiles...)
if err != nil {
return obiseq.NilIPairedBioSequenceBatch, err
return obiiter.NilIPairedBioSequenceBatch, err
}
reverse, err := obiconvert.ReadBioSequencesBatch(_ReverseFiles...)
if err != nil {
return obiseq.NilIPairedBioSequenceBatch, err
return obiiter.NilIPairedBioSequenceBatch, err
}
paired := forward.PairWith(reverse)
pkg/obitools/obipairing/pairing.go
+8 -5
View File
@@ -7,6 +7,7 @@ import (
"runtime"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"github.com/schollz/progressbar/v3"
)
@@ -202,8 +203,10 @@ func AssemblePESequences(seqA, seqB *obiseq.BioSequence,
// The function returns an iterator over batches of obiseq.Biosequence object.
// each pair of processed sequences produces one sequence in the result iterator.
//
func IAssemblePESequencesBatch(iterator obiseq.IPairedBioSequenceBatch,
gap float64, delta, minOverlap int, minIdentity float64, withStats bool, sizes ...int) obiseq.IBioSequenceBatch {
func IAssemblePESequencesBatch(iterator obiiter.IPairedBioSequenceBatch,
gap float64, delta, minOverlap int,
minIdentity float64,
withStats bool, sizes ...int) obiiter.IBioSequenceBatch {
nworkers := runtime.NumCPU() * 3 / 2
buffsize := iterator.BufferSize()
@@ -216,7 +219,7 @@ func IAssemblePESequencesBatch(iterator obiseq.IPairedBioSequenceBatch,
buffsize = sizes[1]
}
newIter := obiseq.MakeIBioSequenceBatch(buffsize)
newIter := obiiter.MakeIBioSequenceBatch(buffsize)
newIter.Add(nworkers)
@@ -233,7 +236,7 @@ func IAssemblePESequencesBatch(iterator obiseq.IPairedBioSequenceBatch,
progressbar.OptionShowIts(),
progressbar.OptionSetDescription("[Sequence Pairing]"))
f := func(iterator obiseq.IPairedBioSequenceBatch, wid int) {
f := func(iterator obiiter.IPairedBioSequenceBatch, wid int) {
arena := obialign.MakePEAlignArena(150, 150)
for iterator.Next() {
@@ -249,7 +252,7 @@ func IAssemblePESequencesBatch(iterator obiseq.IPairedBioSequenceBatch,
}
}
bar.Add(batch.Length() - processed)
newIter.Push(obiseq.MakeBioSequenceBatch(
newIter.Push(obiiter.MakeBioSequenceBatch(
batch.Order(),
cons,
))