Produce less weird crash on non existing files

Former-commit-id: 74bb27bd53c685be530632994bd2ba24c1f362e1

pkg/obiformats/genbank_read.go

@@ -47,7 +47,7 @@ func _ParseGenbankFile(input <-chan _FileChunk, out obiiter.IBioSequence) {
 			nl++
 			line := scanner.Text()
 			switch {
-			case state==inDefinition && ! strings.HasPrefix(line, "            "):
+			case state == inDefinition && !strings.HasPrefix(line, "            "):
 				state = inEntry
 				fallthrough
 			case strings.HasPrefix(line, "LOCUS       "):
@@ -61,7 +61,7 @@ func _ParseGenbankFile(input <-chan _FileChunk, out obiiter.IBioSequence) {
 			case strings.HasPrefix(line, "FEATURES    "):
 				featBytes.WriteString(line)
 				state = inFeature
-			case strings.HasPrefix(line, "ORIGIN      "):
+			case strings.HasPrefix(line, "ORIGIN"):
 				state = inSequence
 			case line == "//":
 				log.Debugln("Total lines := ", nl)
@@ -76,12 +76,15 @@ func _ParseGenbankFile(input <-chan _FileChunk, out obiiter.IBioSequence) {
 				annot["scientific_name"] = scientificName
 				annot["taxid"] = taxid
 				// log.Println(FormatFasta(sequence, FormatFastSeqJsonHeader))
+				log.Debugf("Read sequences %s: %dbp (%d)", sequence.Id(),
+					sequence.Len(), seqBytes.Len())
+
 				sequences = append(sequences, sequence)
 				defBytes = new(bytes.Buffer)
 				featBytes = new(bytes.Buffer)
 				seqBytes = new(bytes.Buffer)
-				nl=0
-				sl=0
+				nl = 0
+				sl = 0
 			default:
 				switch state {
 				case inDefinition:

pkg/obiformats/universal_read.go

@@ -85,8 +85,8 @@ func ReadSequencesFromFile(filename string,
 	switch filetype {
 	case "fastq", "fasta":
 		file.Close()
-		is, _ := ReadFastSeqFromFile(filename, options...)
-		return is, nil
+		is, err := ReadFastSeqFromFile(filename, options...)
+		return is, err
 	case "ecopcr":
 		return ReadEcoPCR(reader, options...), nil
 	case "embl":

pkg/obiseq/class.go

@@ -90,7 +90,7 @@ func AnnotationClassifier(key string, na string) *BioSequenceClassifier {
 		return AnnotationClassifier(key, na)
 	}
 
-	c := BioSequenceClassifier{code, value, reset, clone,"AnnotationClassifier"}
+	c := BioSequenceClassifier{code, value, reset, clone, "AnnotationClassifier"}
 	return &c
 }
 
@@ -127,7 +127,7 @@ func DualAnnotationClassifier(key1, key2 string, na string) *BioSequenceClassifi
 						val2 = fmt.Sprint(value)
 					}
 				} else {
-					val2=na
+					val2 = na
 				}
 			}
 		}
@@ -173,7 +173,7 @@ func DualAnnotationClassifier(key1, key2 string, na string) *BioSequenceClassifi
 		return DualAnnotationClassifier(key1, key2, na)
 	}
 
-	c := BioSequenceClassifier{code, value, reset, clone,"DualAnnotationClassifier"}
+	c := BioSequenceClassifier{code, value, reset, clone, "DualAnnotationClassifier"}
 	return &c
 }
 
@@ -206,7 +206,7 @@ func PredicateClassifier(predicate SequencePredicate) *BioSequenceClassifier {
 		return PredicateClassifier(predicate)
 	}
 
-	c := BioSequenceClassifier{code, value, reset, clone,"PredicateClassifier"}
+	c := BioSequenceClassifier{code, value, reset, clone, "PredicateClassifier"}
 	return &c
 }
 
@@ -228,7 +228,7 @@ func HashClassifier(size int) *BioSequenceClassifier {
 		return HashClassifier(size)
 	}
 
-	c := BioSequenceClassifier{code, value, reset, clone,"HashClassifier"}
+	c := BioSequenceClassifier{code, value, reset, clone, "HashClassifier"}
 	return &c
 }
 
@@ -283,7 +283,7 @@ func SequenceClassifier() *BioSequenceClassifier {
 		return SequenceClassifier()
 	}
 
-	c := BioSequenceClassifier{code, value, reset, clone,"SequenceClassifier"}
+	c := BioSequenceClassifier{code, value, reset, clone, "SequenceClassifier"}
 	return &c
 }
 
@@ -313,7 +313,6 @@ func RotateClassifier(size int) *BioSequenceClassifier {
 		return RotateClassifier(size)
 	}
 
-	c := BioSequenceClassifier{code, value, reset, clone,"RotateClassifier"}
+	c := BioSequenceClassifier{code, value, reset, clone, "RotateClassifier"}
 	return &c
 }
-

pkg/obitools/obiconvert/sequence_reader.go

@@ -1,6 +1,7 @@
 package obiconvert
 
 import (
+	"fmt"
 	"os"
 	"path/filepath"
 	"strings"
@@ -20,6 +21,9 @@ func _ExpandListOfFiles(check_ext bool, filenames ...string) ([]string, error) {
 		err = filepath.Walk(fn,
 			func(path string, info os.FileInfo, err error) error {
 				var e error
+				if info == nil {
+					return fmt.Errorf("cannot open path")
+				}
 				for info.Mode()&os.ModeSymlink == os.ModeSymlink {
 					path, e = filepath.EvalSymlinks(path)
 					if e != nil {