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Patch rev complement and first implementation of --auto in obicsv

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Former-commit-id: f3020e81283b1073c4d1c2d2ff0887e3998e6764
This commit is contained in:
Eric Coissac
2023-11-07 09:37:07 +02:00
parent 6a6a6f6f2c
commit 61c30f9b6a
21 changed files with 270 additions and 107 deletions
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27
pkg/obiseq/biosequence.go
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@@ -15,6 +15,7 @@ import (
"sync"
"sync/atomic"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
log "github.com/sirupsen/logrus"
)
@@ -55,8 +56,7 @@ type Annotation map[string]interface{}
// A BioSequence is a sequence of bytes with an identifier, a definition, a sequence, qualities,
// features and annotations. It aims to represent a biological sequence
type BioSequence struct {
id string // The identidier of the sequence (private accessible through the method Id)
//definition string // The documentation of the sequence (private accessible through the method Definition)
id string // The identidier of the sequence (private accessible through the method Id)
source string // The filename without directory name and extension from where the sequence was read.
sequence []byte // The sequence itself, it is accessible by the methode Sequence
qualities []byte // The quality scores of the sequence.
@@ -188,6 +188,14 @@ func (s *BioSequence) Definition() string {
return definition
}
// HasSequence checks if the BioSequence has a sequence.
//
// No parameters.
// Returns a boolean.
func (s *BioSequence) HasSequence() bool {
return s.sequence != nil && len(s.sequence) > 0
}
// Sequence returns the sequence of the BioSequence.
//
// Returns:
@@ -217,7 +225,7 @@ func (s *BioSequence) Len() int {
// This function does not have any parameters.
// It returns a boolean value indicating whether the BioSequence has qualities.
func (s *BioSequence) HasQualities() bool {
return len(s.qualities) > 0
return s.qualities != nil && len(s.qualities) > 0
}
// Qualities returns the sequence quality scores of the BioSequence.
@@ -235,6 +243,19 @@ func (s *BioSequence) Qualities() Quality {
return __make_default_qualities__(len(s.sequence))
}
// QualitiesString returns the string representation of the qualities of the BioSequence.
//
// Returns a string representing the qualities of the BioSequence after applying the shift.
func (s *BioSequence) QualitiesString() string {
quality_shift := obioptions.OutputQualityShift()
qual := s.Qualities()
qual_ascii := make([]byte, len(qual))
for i := 0; i < len(qual); i++ {
qual_ascii[i] = byte(qual[i] + byte(quality_shift))
}
return string(qual_ascii)
}
// Features returns the feature string of the BioSequence.
//
// The feature string contains the EMBL/GenBank not parsed feature table