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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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14
pkg/obiformats/fastaseq_read.go
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@@ -39,7 +39,7 @@ func EndOfLastFastaEntry(buffer []byte) int {
return last
}
func FastaChunkParser() func(string, io.Reader) (obiseq.BioSequenceSlice, error) {
func FastaChunkParser(UtoT bool) func(string, io.Reader) (obiseq.BioSequenceSlice, error) {
parser := func(source string, input io.Reader) (obiseq.BioSequenceSlice, error) {
var identifier string
@@ -131,7 +131,9 @@ func FastaChunkParser() func(string, io.Reader) (obiseq.BioSequenceSlice, error)
if C >= 'A' && C <= 'Z' {
C = C + 'a' - 'A'
}
if UtoT && C == 'u' {
C = 't'
}
if (C >= 'a' && C <= 'z') || C == '-' || C == '.' || C == '[' || C == ']' {
seqBytes.WriteByte(C)
} else {
@@ -170,6 +172,9 @@ func FastaChunkParser() func(string, io.Reader) (obiseq.BioSequenceSlice, error)
if C >= 'A' && C <= 'Z' {
C = C + 'a' - 'A'
}
if UtoT && C == 'u' {
C = 't'
}
// Removing white space from the sequence
if (C >= 'a' && C <= 'z') || C == '-' || C == '.' || C == '[' || C == ']' {
seqBytes.WriteByte(C)
@@ -207,9 +212,10 @@ func FastaChunkParser() func(string, io.Reader) (obiseq.BioSequenceSlice, error)
func _ParseFastaFile(
input ChannelFileChunk,
out obiiter.IBioSequence,
UtoT bool,
) {
parser := FastaChunkParser()
parser := FastaChunkParser(UtoT)
for chunks := range input {
sequences, err := parser(chunks.Source, chunks.Raw)
@@ -243,7 +249,7 @@ func ReadFasta(reader io.Reader, options ...WithOption) (obiiter.IBioSequence, e
for i := 0; i < nworker; i++ {
out.Add(1)
go _ParseFastaFile(chkchan, out)
go _ParseFastaFile(chkchan, out, opt.UtoT())
}
go func() {