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Patch a bug in the genbank reader for the sequence longer than 10kb.

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This commit is contained in:
Eric Coissac
2023-02-17 10:54:03 +01:00
parent ed87f821eb
commit 8458c0cd8b
2 changed files with 41 additions and 34 deletions
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56
pkg/obiformats/genbank_read.go
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@ -31,6 +31,7 @@ func _ParseGenbankFile(input <-chan _FileChunk, out obiiter.IBioSequence) {
state := inHeader
for chunks := range input {
log.Debugln("Chunk size", (chunks.raw.(*bytes.Buffer)).Len())
scanner := bufio.NewScanner(chunks.raw)
order := chunks.order
sequences := make(obiseq.BioSequenceSlice, 0, 100)
@ -40,15 +41,15 @@ func _ParseGenbankFile(input <-chan _FileChunk, out obiiter.IBioSequence) {
featBytes := new(bytes.Buffer)
seqBytes := new(bytes.Buffer)
taxid := 1
nl := 0
sl := 0
for scanner.Scan() {
nl++
line := scanner.Text()
if !strings.HasPrefix(line, " ") && state != inHeader {
state = inEntry
}
switch {
case state==inDefinition && ! strings.HasPrefix(line, " "):
state = inEntry
fallthrough
case strings.HasPrefix(line, "LOCUS "):
state = inEntry
id = strings.SplitN(line[12:], " ", 2)[0]
@ -62,27 +63,8 @@ func _ParseGenbankFile(input <-chan _FileChunk, out obiiter.IBioSequence) {
state = inFeature
case strings.HasPrefix(line, "ORIGIN "):
state = inSequence
case strings.HasPrefix(line, " "):
switch state {
case inDefinition:
defBytes.WriteByte(' ')
defBytes.WriteString(strings.TrimSpace(line[5:]))
case inFeature:
featBytes.WriteByte('\n')
featBytes.WriteString(line)
if strings.HasPrefix(line, ` /db_xref="taxon:`) {
taxid, _ = strconv.Atoi(strings.SplitN(line[37:], `"`, 2)[0])
}
case inSequence:
parts := strings.SplitN(line[10:], " ", 7)
lparts := len(parts)
for i := 0; i < lparts; i++ {
seqBytes.WriteString(parts[i])
}
default: // Do nothing
}
case line == "//":
log.Debugln("Total lines := ", nl)
sequence := obiseq.NewBioSequence(id,
bytes.ToLower(seqBytes.Bytes()),
defBytes.String())
@ -98,7 +80,29 @@ func _ParseGenbankFile(input <-chan _FileChunk, out obiiter.IBioSequence) {
defBytes = new(bytes.Buffer)
featBytes = new(bytes.Buffer)
seqBytes = new(bytes.Buffer)
nl=0
sl=0
default:
switch state {
case inDefinition:
defBytes.WriteByte(' ')
defBytes.WriteString(strings.TrimSpace(line[5:]))
case inFeature:
featBytes.WriteByte('\n')
featBytes.WriteString(line)
if strings.HasPrefix(line, ` /db_xref="taxon:`) {
taxid, _ = strconv.Atoi(strings.SplitN(line[37:], `"`, 2)[0])
}
case inSequence:
sl++
parts := strings.SplitN(line[10:], " ", 7)
lparts := len(parts)
for i := 0; i < lparts; i++ {
seqBytes.WriteString(parts[i])
}
}
}
}
out.Push(obiiter.MakeBioSequenceBatch(order, sequences))
}