obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-06-29 16:20:46 +00:00
Code Issues Packages Projects Releases Wiki Activity

Adds the --silent-warning options to the obitools commands and removes the --pared-with option from some of the obitols commands.

Browse Source
This commit is contained in:
Eric Coissac
2025-03-25 16:44:46 +01:00
parent 2ab6f67d58
commit 5a3705b6bb
52 changed files with 151 additions and 90 deletions
Download Patch File Download Diff File Expand all files Collapse all files

8
pkg/obiseq/attributes.go
View File

@ -4,6 +4,7 @@ import (
"fmt"
"strconv"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilog"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
log "github.com/sirupsen/logrus"
)
@ -136,7 +137,12 @@ func (s *BioSequence) SetAttribute(key string, value interface{}) {
}
if key == "sequence" {
s.SetSequence(value.([]byte))
data, err := obiutils.InterfaceToString(value)
if err != nil {
obilog.Warnf("%s: cannot convert value %v to sequence", s.Id(), value)
return
}
s.SetSequence([]byte(data))
return
}

9
pkg/obiseq/biosequence.go
View File

@ -444,6 +444,15 @@ func (s *BioSequence) SetSequence(sequence []byte) {
s.sequence = obiutils.InPlaceToLower(CopySlice(sequence))
}
func (s *BioSequence) HasValidSequence() bool {
for _, c := range s.sequence {
if !((c >= 'a' && c <= 'z') || c == '-' || c == '.' || c == '[' || c == ']') {
return false
}
}
return true
}
// Setting the qualities of the BioSequence.
func (s *BioSequence) SetQualities(qualities Quality) {
if s.qualities != nil {

3
pkg/obiseq/biosequenceslice.go
View File

@ -1,6 +1,7 @@
package obiseq
import (
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilog"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
log "github.com/sirupsen/logrus"
@ -61,7 +62,7 @@ func (s *BioSequenceSlice) EnsureCapacity(capacity int) *BioSequenceSlice {
if c < capacity {
n++
if n < 4 {
log.Warnf("cannot allocate a Biosequence Slice of size %d (only %d from %d)", capacity, c, old_c)
obilog.Warnf("cannot allocate a Biosequence Slice of size %d (only %d from %d)", capacity, c, old_c)
} else {
log.Panicf("cannot allocate a Biosequence Slice of size %d (only %d from %d)", capacity, c, old_c)
}

4
pkg/obiseq/predicate.go
View File

@ -5,6 +5,7 @@ import (
"fmt"
"regexp"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilog"
log "github.com/sirupsen/logrus"
)
@ -278,9 +279,10 @@ func ExpressionPredicat(expression string) SequencePredicate {
)
if err != nil {
log.Fatalf("Expression '%s' cannot be evaluated on sequence %s",
obilog.Warnf("Expression '%s' cannot be evaluated on sequence %s",
expression,
sequence.Id())
return false
}
return value

7
pkg/obiseq/taxonomy_methods.go
View File

@ -6,6 +6,7 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilog"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
@ -41,7 +42,7 @@ func (s *BioSequence) SetTaxid(taxid string, rank ...string) {
taxon, isAlias, err = taxonomy.Taxon(taxid)
if err != nil {
logger := log.Warnf
logger := obilog.Warnf
if obidefault.FailOnTaxonomy() {
logger = log.Fatalf
}
@ -51,7 +52,7 @@ func (s *BioSequence) SetTaxid(taxid string, rank ...string) {
if isAlias {
if obidefault.UpdateTaxid() {
log.Warnf("%s: Taxid: %v is updated to %s",
obilog.Warnf("%s: Taxid: %v is updated to %s",
s.Id(), taxid, taxon.String())
taxid = taxon.String()
} else {
@ -59,7 +60,7 @@ func (s *BioSequence) SetTaxid(taxid string, rank ...string) {
log.Fatalf("%s: Taxid: %v is an alias from taxonomy (%v) to %s",
s.Id(), taxid, taxonomy.Name(), taxon.String())
}
log.Warnf("%s: Taxid %v has to be updated to %s",
obilog.Warnf("%s: Taxid %v has to be updated to %s",
s.Id(), taxid, taxon.String())
}

3
pkg/obiseq/taxonomy_predicate.go
View File

@ -3,6 +3,7 @@ package obiseq
import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilog"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
@ -66,7 +67,7 @@ func IsSubCladeOfSlot(taxonomy *obitax.Taxonomy, key string) SequencePredicate {
parent, _, err := taxonomy.Taxon(val)
if err != nil {
log.Warnf("%s: %s is unkown from the taxonomy (%v)", sequence.Id(), val, err)
obilog.Warnf("%s: %s is unkown from the taxonomy (%v)", sequence.Id(), val, err)
}
taxon := sequence.Taxon(taxonomy)

6
pkg/obiseq/worker.go
View File

@ -4,7 +4,7 @@ import (
"fmt"
"slices"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilog"
)
type SeqAnnotator func(*BioSequence)
@ -119,7 +119,7 @@ func SeqToSliceWorker(worker SeqWorker,
s.Id(), err)
return BioSequenceSlice{}, err
} else {
log.Warnf("got an error on sequence %s processing : %v",
obilog.Warnf("got an error on sequence %s processing : %v",
s.Id(), err)
}
}
@ -208,7 +208,7 @@ func SeqToSliceConditionalWorker(
s.Id(), err)
return BioSequenceSlice{}, err
} else {
log.Warnf("got an error on sequence %s processing : %v",
obilog.Warnf("got an error on sequence %s processing : %v",
s.Id(), err)
}
}