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Change path of the obitools pkg

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Former-commit-id: 311cbf8df3b990b393c6f4885d62e74564423b65
This commit is contained in:
Eric Coissac
2023-11-29 12:14:37 +01:00
parent 72ad84c2d4
commit 8d77cc4133
122 changed files with 1004 additions and 544 deletions
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22
pkg/obitools/obiconsensus/obiconsensus.go
View File

@@ -8,11 +8,11 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obikmer"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obisuffix"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obikmer"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obisuffix"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
func BuildConsensus(seqs obiseq.BioSequenceSlice,
@@ -83,20 +83,20 @@ func BuildConsensus(seqs obiseq.BioSequenceSlice,
}
graph.FilterMin(threshold)
log.Printf("Graph size : %d\n", graph.Len())
if save_graph {
file, err := os.Create(path.Join(dirname,
fmt.Sprintf("%s.gml", seqs[0].Source())))
if err != nil {
fmt.Println(err)
} else {
file.WriteString(graph.Gml())
file.Close()
}
}
}
seq, err := graph.LongestConsensus(seqs[0].Source())
@@ -122,11 +122,11 @@ func Consensus(iterator obiiter.IBioSequence) obiiter.IBioSequence {
// path does not exist or is not directory
os.RemoveAll(dirname)
err := os.Mkdir(dirname, 0755)
if err != nil {
log.Panicf("Cannot create directory %s for saving graphs", dirname)
}
}
}
}
newIter.Add(1)

4
pkg/obitools/obiconsensus/options.go
View File

@@ -1,7 +1,7 @@
package obiconsensus
import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"github.com/DavidGamba/go-getoptions"
)
@@ -66,4 +66,4 @@ func CLIKmerDepth() float64 {
func CLIThreshold() float64 {
return _threshold
}
}