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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/embl_read.go
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@@ -87,7 +87,7 @@ func EndOfLastFlatFileEntry(buff []byte) int {
return -1
}
func EmblChunkParser(withFeatureTable bool) func(string, io.Reader) (obiseq.BioSequenceSlice, error) {
func EmblChunkParser(withFeatureTable, UtoT bool) func(string, io.Reader) (obiseq.BioSequenceSlice, error) {
parser := func(source string, input io.Reader) (obiseq.BioSequenceSlice, error) {
scanner := bufio.NewScanner(input)
sequences := make(obiseq.BioSequenceSlice, 0, 100)
@@ -128,6 +128,9 @@ func EmblChunkParser(withFeatureTable bool) func(string, io.Reader) (obiseq.BioS
parts := strings.SplitN(line[5:], " ", 7)
np := len(parts) - 1
for i := 0; i < np; i++ {
if UtoT {
parts[i] = strings.ReplaceAll(parts[i], "u", "t")
}
seqBytes.WriteString(parts[i])
}
case line == "//":
@@ -161,10 +164,10 @@ func EmblChunkParser(withFeatureTable bool) func(string, io.Reader) (obiseq.BioS
func _ParseEmblFile(
input ChannelFileChunk,
out obiiter.IBioSequence,
withFeatureTable bool,
withFeatureTable, UtoT bool,
) {
parser := EmblChunkParser(withFeatureTable)
parser := EmblChunkParser(withFeatureTable, UtoT)
for chunks := range input {
order := chunks.Order
@@ -206,6 +209,7 @@ func ReadEMBL(reader io.Reader, options ...WithOption) (obiiter.IBioSequence, er
entry_channel,
newIter,
opt.WithFeatureTable(),
opt.UtoT(),
)
}