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Work on iterators and recycling of biosequences

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This commit is contained in:
Eric Coissac
2022-01-14 23:11:36 +01:00
parent ef66ca4972
commit e8fff6477b
22 changed files with 350 additions and 111 deletions
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57
pkg/obiformats/universal_write.go
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@ -52,28 +52,45 @@ func WriteSequencesToStdout(iterator obiseq.IBioSequence, options ...WithOption)
return WriteSequences(iterator, os.Stdout, options...)
}
// func WriteSequenceBatch(iterator obiseq.IBioSequenceBatch,
// file io.Writer,
// options ...WithOption) error {
func WriteSequenceBatch(iterator obiseq.IBioSequenceBatch,
file io.Writer,
options ...WithOption) (obiseq.IBioSequenceBatch,error) {
// opts := MakeOptions(options)
var newIter obiseq.IBioSequenceBatch
var err error
// header_format := opts.FormatFastSeqHeader()
// quality := opts.QualityShift()
ok := iterator.Next()
// ok := iterator.Next()
if ok {
iterator.PushBack()
batch := iterator.Get()
if batch.Slice()[0].HasQualities() {
newIter,err = WriteFastqBatch(iterator, file, options...)
} else {
newIter,err = WriteFastaBatch(iterator, file, options...)
}
// if ok {
// batch := iterator.Get()
// if batch.Slice()[0].HasQualities() {
// file.Write()
// fmt.Fprintln(file, FormatFastq(seq, quality, header_format))
// WriteFastq(iterator, file, options...)
// } else {
// fmt.Fprintln(file, FormatFasta(seq, header_format))
// WriteFasta(iterator, file, options...)
// }
// }
return newIter,err
}
// return nil
// }
return obiseq.NilIBioSequenceBatch,fmt.Errorf("input iterator not ready")
}
func WriteSequencesBatchToStdout(iterator obiseq.IBioSequenceBatch,
options ...WithOption) (obiseq.IBioSequenceBatch,error) {
return WriteSequenceBatch(iterator, os.Stdout, options...)
}
func WriteSequencesBatchToFile(iterator obiseq.IBioSequenceBatch,
filename string,
options ...WithOption) (obiseq.IBioSequenceBatch,error) {
file, err := os.Create(filename)
if err != nil {
log.Fatalf("open file error: %v", err)
return obiseq.NilIBioSequenceBatch, err
}
return WriteSequenceBatch(iterator, file, options...)
}