Start to use leveled log

pkg/obiformats/dispatcher.go

@@ -2,7 +2,7 @@ package obiformats
 
 import (
 	"fmt"
-	"log"
+	log "github.com/sirupsen/logrus"
 	"sync"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"

pkg/obiformats/ecopcr_read.go

@@ -5,7 +5,7 @@ import (
 	"encoding/csv"
 	"fmt"
 	"io"
-	"log"
+	log "github.com/sirupsen/logrus"
 	"os"
 	"strconv"
 	"strings"

pkg/obiformats/embl_read.go

@@ -5,7 +5,7 @@ import (
 	"bytes"
 	"compress/gzip"
 	"io"
-	"log"
+	log "github.com/sirupsen/logrus"
 	"os"
 	"strconv"
 	"strings"

pkg/obiformats/fastseq_json_header.go

@@ -1,7 +1,7 @@
 package obiformats
 
 import (
-	"log"
+	log "github.com/sirupsen/logrus"
 	"strings"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"

pkg/obiformats/fastseq_read.go

@@ -8,10 +8,11 @@ import "C"
 
 import (
 	"fmt"
-	"log"
 	"os"
 	"unsafe"
 
+	log "github.com/sirupsen/logrus"
+
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/cutils"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
@@ -61,7 +62,7 @@ func _FastseqReader(seqfile C.fast_kseq_p,
 		slice = append(slice, rep)
 		ii++
 		if ii >= batch_size {
-			// log.Printf("\n==> Pushing sequence batch\n")
+			//log.Printf("\n==> Pushing sequence batch\n")
 			// start := time.Now()
 
 			iterator.Push(obiiter.MakeBioSequenceBatch(i, slice))
@@ -100,7 +101,7 @@ func ReadFastSeqBatchFromFile(filename string, options ...WithOption) (obiiter.I
 	fi, err := os.Stat(filename)
 	if err == nil {
 		size = fi.Size()
-		log.Printf("File size of %s is %d bytes\n", filename, size)
+		log.Debugf("File size of %s is %d bytes\n", filename, size)
 	} else {
 		size = -1
 	}
@@ -110,10 +111,10 @@ func ReadFastSeqBatchFromFile(filename string, options ...WithOption) (obiiter.I
 
 	go func() {
 		newIter.WaitAndClose()
-		log.Println("End of the fastq file reading")
+		log.Debugln("End of the fastq file reading")
 	}()
 
-	log.Println("Start of the fastq file reading")
+	log.Debugln("Start of the fastq file reading")
 
 	go _FastseqReader(pointer, newIter, opt.BatchSize())
 	parser := opt.ParseFastSeqHeader()

pkg/obiformats/fastseq_write_fasta.go

@@ -4,10 +4,11 @@ import (
 	"bytes"
 	"fmt"
 	"io"
-	"log"
 	"os"
 	"strings"
 
+	log "github.com/sirupsen/logrus"
+
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 )
@@ -114,6 +115,7 @@ func WriteFastaBatch(iterator obiiter.IBioSequenceBatch,
 	go func() {
 		newIter.WaitAndClose()
 		close(chunkchan)
+		log.Debugln("End of the fasta file writing")
 	}()
 
 	ff := func(iterator obiiter.IBioSequenceBatch) {
@@ -128,7 +130,7 @@ func WriteFastaBatch(iterator obiiter.IBioSequenceBatch,
 		newIter.Done()
 	}
 
-	log.Println("Start of the fasta file writing")
+	log.Debugln("Start of the fasta file writing")
 	go ff(iterator)
 	for i := 0; i < nwriters-1; i++ {
 		go ff(iterator.Split())

pkg/obiformats/fastseq_write_fastq.go

@@ -4,10 +4,11 @@ import (
 	"bytes"
 	"fmt"
 	"io"
-	"log"
 	"os"
 	"time"
 
+	log "github.com/sirupsen/logrus"
+
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 )
@@ -114,6 +115,7 @@ func WriteFastqBatch(iterator obiiter.IBioSequenceBatch,
 			time.Sleep(time.Millisecond)
 		}
 		close(chunkchan)
+		log.Debugln("End of the fastq file writing")
 	}()
 
 	ff := func(iterator obiiter.IBioSequenceBatch) {
@@ -129,7 +131,7 @@ func WriteFastqBatch(iterator obiiter.IBioSequenceBatch,
 		newIter.Done()
 	}
 
-	log.Println("Start of the fastq file writing")
+	log.Debugln("Start of the fastq file writing")
 	go ff(iterator)
 	for i := 0; i < nwriters-1; i++ {
 		go ff(iterator.Split())

pkg/obiformats/ncbitaxdump/read.go

@@ -5,7 +5,7 @@ import (
 	"encoding/csv"
 	"fmt"
 	"io"
-	"log"
+	log "github.com/sirupsen/logrus"
 	"os"
 	"path"
 	"strconv"

pkg/obiformats/universal_read.go

@@ -4,10 +4,11 @@ import (
 	"bufio"
 	"compress/gzip"
 	"io"
-	"log"
 	"os"
 	"strings"
 
+	log "github.com/sirupsen/logrus"
+
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 )
 
@@ -57,7 +58,7 @@ func ReadSequencesBatchFromFile(filename string,
 	if err != nil {
 		file.Seek(0, 0)
 	} else {
-		log.Printf("File %s is gz compressed ", filename)
+		log.Debugf("File %s is gz compressed ", filename)
 		reader = greader
 	}
 
@@ -72,7 +73,7 @@ func ReadSequencesBatchFromFile(filename string,
 	}
 
 	filetype := GuessSeqFileType(string(tag))
-	log.Printf("File guessed format : %s (tag: %s)",
+	log.Debug("File guessed format : %s (tag: %s)",
 		filetype, (strings.Split(string(tag), "\n"))[0])
 	reader = breader
 

pkg/obiformats/universal_write.go

@@ -3,7 +3,7 @@ package obiformats
 import (
 	"fmt"
 	"io"
-	"log"
+	log "github.com/sirupsen/logrus"
 	"os"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"