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Changes to be committed:

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modified:   cmd/obitools/obitag/main.go
	modified:   cmd/obitools/obitaxonomy/main.go
	modified:   pkg/obiformats/csvtaxdump_read.go
	modified:   pkg/obiformats/ecopcr_read.go
	modified:   pkg/obiformats/ncbitaxdump_read.go
	modified:   pkg/obiformats/ncbitaxdump_readtar.go
	modified:   pkg/obiformats/newick_write.go
	modified:   pkg/obiformats/options.go
	modified:   pkg/obiformats/taxonomy_read.go
	modified:   pkg/obiformats/universal_read.go
	modified:   pkg/obiiter/extract_taxonomy.go
	modified:   pkg/obioptions/options.go
	modified:   pkg/obioptions/version.go
	new file:   pkg/obiphylo/tree.go
	modified:   pkg/obiseq/biosequenceslice.go
	modified:   pkg/obiseq/taxonomy_methods.go
	modified:   pkg/obitax/taxonomy.go
	modified:   pkg/obitax/taxonset.go
	modified:   pkg/obitools/obiconvert/sequence_reader.go
	modified:   pkg/obitools/obitag/obitag.go
	modified:   pkg/obitools/obitaxonomy/obitaxonomy.go
	modified:   pkg/obitools/obitaxonomy/options.go
	deleted:    sample/.DS_Store
This commit is contained in:
Eric Coissac
2025-06-04 09:48:10 +02:00
parent 3424d3057f
commit 6cb7a5a352
23 changed files with 230 additions and 56 deletions
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29
pkg/obiformats/ecopcr_read.go
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@ -4,13 +4,10 @@ import (
"encoding/csv"
"fmt"
"io"
"os"
"path"
"strconv"
"strings"
gzip "github.com/klauspost/pgzip"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
@ -177,8 +174,10 @@ func ReadEcoPCR(reader io.Reader, options ...WithOption) (obiiter.IBioSequence,
}()
go func() {
var err error = nil
var seq *obiseq.BioSequence
seq, err := __read_ecopcr_bioseq__(&ecopcr)
seq, err = __read_ecopcr_bioseq__(&ecopcr)
seq.SetSource(opt.Source())
slice := make(obiseq.BioSequenceSlice, 0, opt.BatchSize())
i := 0
@ -194,7 +193,12 @@ func ReadEcoPCR(reader io.Reader, options ...WithOption) (obiiter.IBioSequence,
}
seq, err = __read_ecopcr_bioseq__(&ecopcr)
seq.SetSource(opt.Source())
if err == nil {
seq.SetSource(opt.Source())
} else if err != io.EOF {
log.Panicf("%+v", err)
}
}
if len(slice) > 0 {
@ -218,22 +222,21 @@ func ReadEcoPCR(reader io.Reader, options ...WithOption) (obiiter.IBioSequence,
func ReadEcoPCRFromFile(filename string, options ...WithOption) (obiiter.IBioSequence, error) {
var reader io.Reader
var greader io.Reader
var err error
options = append(options, OptionsSource(obiutils.RemoveAllExt((path.Base(filename)))))
reader, err = os.Open(filename)
reader, err = obiutils.Ropen(filename)
if err == obiutils.ErrNoContent {
log.Infof("file %s is empty", filename)
return ReadEmptyFile(options...)
}
if err != nil {
log.Printf("open file error: %+v", err)
return obiiter.NilIBioSequence, err
}
// Test if the flux is compressed by gzip
greader, err = gzip.NewReader(reader)
if err == nil {
reader = greader
}
return ReadEcoPCR(reader, options...)
}