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Add a reading option on readers to convet U to T

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This commit is contained in:
Eric Coissac
2025-07-07 15:29:07 +02:00
parent 8c26fc9884
commit 8d53d253d4
4 changed files with 34 additions and 13 deletions
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10
pkg/obiformats/genbank_read.go
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@@ -29,7 +29,7 @@ const (
var _seqlenght_rx = regexp.MustCompile(" +([0-9]+) bp")
func GenbankChunkParser(withFeatureTable bool) func(string, io.Reader) (obiseq.BioSequenceSlice, error) {
func GenbankChunkParser(withFeatureTable, UtoT bool) func(string, io.Reader) (obiseq.BioSequenceSlice, error) {
return func(source string, input io.Reader) (obiseq.BioSequenceSlice, error) {
state := inHeader
scanner := bufio.NewReader(input)
@@ -165,6 +165,9 @@ func GenbankChunkParser(withFeatureTable bool) func(string, io.Reader) (obiseq.B
parts := strings.SplitN(line[10:], " ", 6)
lparts := len(parts)
for i := 0; i < lparts; i++ {
if UtoT {
parts[i] = strings.ReplaceAll(parts[i], "u", "t")
}
seqBytes.WriteString(parts[i])
}
processed = true
@@ -200,9 +203,9 @@ func GenbankChunkParser(withFeatureTable bool) func(string, io.Reader) (obiseq.B
func _ParseGenbankFile(input ChannelFileChunk,
out obiiter.IBioSequence,
withFeatureTable bool) {
withFeatureTable, UtoT bool) {
parser := GenbankChunkParser(withFeatureTable)
parser := GenbankChunkParser(withFeatureTable, UtoT)
for chunks := range input {
sequences, err := parser(chunks.Source, chunks.Raw)
@@ -242,6 +245,7 @@ func ReadGenbank(reader io.Reader, options ...WithOption) (obiiter.IBioSequence,
entry_channel,
newIter,
opt.WithFeatureTable(),
opt.UtoT(),
)
}