Add some option to the obiconsensus command

Former-commit-id: cf30a404a4943e4527106c977b01712ef454e028

cmd/obitools/obiconsensus/main.go

@@ -13,7 +13,7 @@ import (
 )
 
 func main() {
-	optionParser := obioptions.GenerateOptionParser(obiconvert.OptionSet)
+	optionParser := obioptions.GenerateOptionParser(obiconsensus.OptionSet)
 
 	_, args := optionParser(os.Args)
 	obiconvert.SetFullFileBatch()
@@ -25,7 +25,7 @@ func main() {
 		os.Exit(1)
 	}
 
-	consensus := obiconsensus.Consensus(fs, 0.95)
+	consensus := obiconsensus.Consensus(fs)
 	obiconvert.CLIWriteBioSequences(consensus, true)
 
 	obiiter.WaitForLastPipe()

pkg/obitools/obiconsensus/obiconsensus.go

@@ -1,6 +1,9 @@
 package obiconsensus
 
 import (
+	"fmt"
+	"os"
+	"path"
 	"sort"
 
 	log "github.com/sirupsen/logrus"
@@ -12,25 +15,30 @@ import (
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
 )
 
-func BuildConsensus(seqs obiseq.BioSequenceSlice, quorum float64) (*obiseq.BioSequence, error) {
+func BuildConsensus(seqs obiseq.BioSequenceSlice,
+	kmer_size int, quorum float64,
+	min_depth float64,
+	save_graph bool, dirname string) (*obiseq.BioSequence, error) {
 
 	log.Printf("Number of reads : %d\n", len(seqs))
 
-	longest := make([]int, len(seqs))
+	if kmer_size < 0 {
+		longest := make([]int, len(seqs))
 
-	for i := range seqs {
-		s := seqs[i : i+1]
-		sa := obisuffix.BuildSuffixArray(&s)
-		longest[i] = obiutils.MaxSlice(sa.CommonSuffix())
+		for i := range seqs {
+			s := seqs[i : i+1]
+			sa := obisuffix.BuildSuffixArray(&s)
+			longest[i] = obiutils.MaxSlice(sa.CommonSuffix())
+		}
+
+		o := obiutils.Order(sort.IntSlice(longest))
+		i := int(float64(len(seqs)) * quorum)
+
+		kmer_size = longest[o[i]] + 1
+		log.Printf("estimated kmer size : %d", kmer_size)
 	}
 
-	o := obiutils.Order(sort.IntSlice(longest))
-	i := int(float64(len(seqs)) * quorum)
-
-	kmersize := longest[o[i]] + 1
-	log.Printf("estimated kmer size : %d", kmersize)
-
-	graph := obikmer.MakeDeBruijnGraph(kmersize)
+	graph := obikmer.MakeDeBruijnGraph(kmer_size)
 
 	for _, s := range seqs {
 		graph.Push(s)
@@ -38,50 +46,64 @@ func BuildConsensus(seqs obiseq.BioSequenceSlice, quorum float64) (*obiseq.BioSe
 
 	log.Printf("Graph size : %d\n", graph.Len())
 	total_kmer := graph.Len()
-	spectrum := graph.LinkSpectrum()
-	cum := make(map[int]int)
-
-	spectrum[1] = 0
-	for i := 2; i < len(spectrum); i++ {
-		spectrum[i] += spectrum[i-1]
-		cum[spectrum[i]]++
-	}
-
-	max := 0
-	kmax := 0
-	for k, obs := range cum {
-		if obs > max {
-			max = obs
-			kmax = k
-		}
-	}
 
 	threshold := 0
-	for i, total := range spectrum {
-		if total == kmax {
-			threshold = i
-			break
+
+	switch {
+	case min_depth < 0:
+		spectrum := graph.LinkSpectrum()
+		cum := make(map[int]int)
+
+		spectrum[1] = 0
+		for i := 2; i < len(spectrum); i++ {
+			spectrum[i] += spectrum[i-1]
+			cum[spectrum[i]]++
 		}
+
+		max := 0
+		kmax := 0
+		for k, obs := range cum {
+			if obs > max {
+				max = obs
+				kmax = k
+			}
+		}
+
+		for i, total := range spectrum {
+			if total == kmax {
+				threshold = i
+				break
+			}
+		}
+		threshold /= 2
+	case min_depth >= 1:
+		threshold = int(min_depth)
+	default:
+		threshold = int(float64(len(seqs)) * min_depth)
 	}
-	threshold /= 2
+
 	graph.FilterMin(threshold)
+
 	log.Printf("Graph size : %d\n", graph.Len())
 
-	// file, err := os.Create(
-	// 	fmt.Sprintf("%s.gml", seqs[0].Source()))
+	if save_graph {
 	
-	// if err != nil {
-	// 	fmt.Println(err)
-	// } else {
-	// 	file.WriteString(graph.GML())
-	// 	file.Close()
-	// }
+		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())
 
 	seq.SetCount(len(seqs))
 	seq.SetAttribute("seq_length", seq.Len())
-	seq.SetAttribute("kmer_size", kmersize)
+	seq.SetAttribute("kmer_size", kmer_size)
 	seq.SetAttribute("kmer_min_occur", threshold)
 	seq.SetAttribute("kmer_max_occur", graph.MaxLink())
 	seq.SetAttribute("filtered_graph_size", graph.Len())
@@ -90,10 +112,23 @@ func BuildConsensus(seqs obiseq.BioSequenceSlice, quorum float64) (*obiseq.BioSe
 	return seq, err
 }
 
-func Consensus(iterator obiiter.IBioSequence, quorum float64) obiiter.IBioSequence {
+func Consensus(iterator obiiter.IBioSequence) obiiter.IBioSequence {
 	newIter := obiiter.MakeIBioSequence()
 	size := 10
 
+	if CLISaveGraphToFiles() {
+		dirname := CLIGraphFilesDirectory()
+		if stat, err := os.Stat(dirname); err != nil || !stat.IsDir() {
+			// 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)
 
 	go func() {
@@ -107,7 +142,12 @@ func Consensus(iterator obiiter.IBioSequence, quorum float64) obiiter.IBioSequen
 
 		for iterator.Next() {
 			seqs := iterator.Get()
-			consensus, err := BuildConsensus(seqs.Slice(), quorum)
+
+			consensus, err := BuildConsensus(seqs.Slice(),
+				CLIKmerSize(), CLIThreshold(),
+				CLIKmerDepth(),
+				CLISaveGraphToFiles(), CLIGraphFilesDirectory(),
+			)
 
 			if err == nil {
 				buffer = append(buffer, consensus)
@@ -118,7 +158,7 @@ func Consensus(iterator obiiter.IBioSequence, quorum float64) obiiter.IBioSequen
 				order++
 				buffer = obiseq.MakeBioSequenceSlice()
 			}
-			seqs.Recycle()
+			seqs.Recycle(true)
 		}
 
 		if len(buffer) > 0 {

pkg/obitools/obiconsensus/options.go

@@ -5,9 +5,65 @@ import (
 	"github.com/DavidGamba/go-getoptions"
 )
 
+var _saveGraph = "__@@NOSAVE@@__"
+var _kmerSize = -1
+var _threshold = 0.99
+var _mindepth = -1.0
+
+func ObiconsensusOptionSet(options *getoptions.GetOpt) {
+
+	options.StringVar(&_saveGraph, "save-graph", _saveGraph,
+		options.Description("Creates a directory containing the set of De Bruijn graphs used by "+
+			"the obiconsensus algorithm. "+
+			"The graph files follow the graphml format."),
+	)
+
+	options.IntVar(&_kmerSize, "kmer-size", _kmerSize,
+		options.ArgName("SIZE"),
+		options.Description("The size of the kmer used to build the consensus. "+
+			"Default value = -1, which means that the kmer size is estimated from the data"),
+	)
+
+	options.Float64Var(&_threshold, "threshold", _threshold,
+		options.ArgName("RATIO"),
+		options.Description("A threshold between O and 1 used to determine the optimal "+
+			"kmer size"),
+	)
+
+	options.Float64Var(&_mindepth, "min-depth", _mindepth,
+		options.ArgName("DEPTH"),
+		options.Description("if DEPTH is between 0 and 1, it corresponds to fraction of the "+
+			"reads in which a kmer must occurs to be conserved in the graph. If DEPTH is greater "+
+			"than 1, indicate the minimum count of occurrence for a kmer to be kept. "+
+			"Default value = -1, which means that the DEPTH is estimated from the data"),
+	)
+
+}
 
 func OptionSet(options *getoptions.GetOpt) {
 	obiconvert.InputOptionSet(options)
 	obiconvert.OutputOptionSet(options)
+	ObiconsensusOptionSet(options)
 }
 
+// Returns true it the obliclean graphs must be saved
+func CLISaveGraphToFiles() bool {
+	return _saveGraph != "__@@NOSAVE@@__"
+}
+
+// It returns the directory where the graph files are saved
+func CLIGraphFilesDirectory() string {
+	return _saveGraph
+}
+
+func CLIKmerSize() int {
+	return _kmerSize
+}
+
+func CLIKmerDepth() float64 {
+	return _mindepth
+}
+
+func CLIThreshold() float64 {
+	return _threshold
+}