obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-12-10 01:30:27 +00:00
Code Issues Packages Projects Releases Wiki Activity

Adds the ability to read gzip-tar file for the taxonomy dump

Browse Source
This commit is contained in:
Eric Coissac
2025-01-24 11:47:59 +01:00
parent ffd67252c3
commit 3137c1f841
17 changed files with 305 additions and 64 deletions
Download Patch File Download Diff File Expand all files Collapse all files

8
pkg/obiformats/fastaseq_read.go
View File

@@ -271,9 +271,9 @@ func ReadFasta(reader io.Reader, options ...WithOption) (obiiter.IBioSequence, e
func ReadFastaFromFile(filename string, options ...WithOption) (obiiter.IBioSequence, error) {
options = append(options, OptionsSource(obiutils.RemoveAllExt((path.Base(filename)))))
file, err := Ropen(filename)
file, err := obiutils.Ropen(filename)
if err == ErrNoContent {
if err == obiutils.ErrNoContent {
log.Infof("file %s is empty", filename)
return ReadEmptyFile(options...)
}
@@ -287,9 +287,9 @@ func ReadFastaFromFile(filename string, options ...WithOption) (obiiter.IBioSequ
func ReadFastaFromStdin(reader io.Reader, options ...WithOption) (obiiter.IBioSequence, error) {
options = append(options, OptionsSource("stdin"))
input, err := Buf(os.Stdin)
input, err := obiutils.Buf(os.Stdin)
if err == ErrNoContent {
if err == obiutils.ErrNoContent {
log.Infof("stdin is empty")
return ReadEmptyFile(options...)
}