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A go implementation of the fasta reader

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Former-commit-id: 603592c4761fb0722e9e0501d78de1bd3ba238fa
This commit is contained in:
Eric Coissac
2023-09-01 09:30:12 +02:00
parent 3f8c0d6a2f
commit 62b57f4ede
15 changed files with 1403 additions and 77 deletions
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18
pkg/obiformats/genbank_read.go
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@ -34,14 +34,14 @@ var _seqlenght_rx = regexp.MustCompile(" +([0-9]+) bp")
func _ParseGenbankFile(source string,
input <-chan _FileChunk, out obiiter.IBioSequence,
chunck_order func() int) {
var err error
var err error
state := inHeader
for chunks := range input {
// log.Debugln("Chunk size", (chunks.raw.(*bytes.Buffer)).Len())
scanner := bufio.NewScanner(chunks.raw)
sequences := make(obiseq.BioSequenceSlice, 0, 100)
sumlength:=0
sumlength := 0
id := ""
lseq := -1
scientificName := ""
@ -61,12 +61,12 @@ func _ParseGenbankFile(source string,
case strings.HasPrefix(line, "LOCUS "):
state = inEntry
id = strings.SplitN(line[12:], " ", 2)[0]
match_length := _seqlenght_rx.FindStringSubmatch(line)
match_length := _seqlenght_rx.FindStringSubmatch(line)
if len(match_length) > 0 {
lseq,err = strconv.Atoi(match_length[1])
lseq, err = strconv.Atoi(match_length[1])
if err != nil {
lseq = -1
}
}
}
if lseq > 0 {
seqBytes = bytes.NewBuffer(obiseq.GetSlice(lseq + 20))
@ -101,7 +101,7 @@ func _ParseGenbankFile(source string,
// sequence.Len(), seqBytes.Len())
sequences = append(sequences, sequence)
sumlength+=sequence.Len()
sumlength += sequence.Len()
if len(sequences) == 100 || sumlength > 1e7 {
out.Push(obiiter.MakeBioSequenceBatch(chunck_order(), sequences))
@ -137,7 +137,7 @@ func _ParseGenbankFile(source string,
if len(sequences) > 0 {
out.Push(obiiter.MakeBioSequenceBatch(chunck_order(), sequences))
}
}
}
out.Done()
@ -159,13 +159,13 @@ func ReadGenbank(reader io.Reader, options ...WithOption) obiiter.IBioSequence {
// for j := 0; j < opt.ParallelWorkers(); j++ {
for j := 0; j < nworkers; j++ {
go _ParseGenbankFile(opt.Source(), entry_channel, newIter,chunck_order)
go _ParseGenbankFile(opt.Source(), entry_channel, newIter, chunck_order)
}
go _ReadFlatFileChunk(reader, entry_channel)
if opt.pointer.full_file_batch {
newIter = newIter.FullFileIterator()
newIter = newIter.CompleteFileIterator()
}
return newIter