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Go implementation of fasta and fastq parser

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Former-commit-id: 3f4fd355c169afbef2d5fef1f5e407aabb71d031
This commit is contained in:
Eric Coissac
2023-09-03 19:16:37 +02:00
parent 6d1ac60c48
commit 5c30ec354f
3 changed files with 370 additions and 21 deletions
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9
pkg/obiformats/universal_read.go
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@ -148,14 +148,15 @@ func ReadSequencesFromFile(filename string,
if err != nil {
return obiiter.NilIBioSequence, err
}
log.Infof("%s mime type: %s", filename, mime.String())
reader = bufio.NewReader(reader)
switch mime.String() {
case "text/fastq":
file.Close()
is, err := ReadFastSeqFromFile(filename, options...)
return is, err
return ReadFastq(reader, options...)
// file.Close()
// is, err := ReadFastSeqFromFile(filename, options...)
// return is, err
case "text/fasta":
return ReadFasta(reader, options...)
case "text/ecopcr2":