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Change the way sequence definition are managed. They are now when present stored as an attribute

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Former-commit-id: 6e618377c05b42937d2eace3c9668390980ab68c
This commit is contained in:
Eric Coissac
2023-10-05 07:21:12 +02:00
parent 5c30ec354f
commit d23a911080
11 changed files with 115 additions and 30 deletions
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9
pkg/obiformats/empty_file.go Normal file
View File

@@ -0,0 +1,9 @@
package obiformats
import "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
func ReadEmptyFile(options ...WithOption) (obiiter.IBioSequence, error) {
out := obiiter.MakeIBioSequence()
out.Close()
return out, nil
}

10
pkg/obiformats/fastaseq_read.go
View File

@@ -294,6 +294,11 @@ func ReadFastaFromFile(filename string, options ...WithOption) (obiiter.IBioSequ
file, err := Ropen(filename)
if err == ErrNoContent {
log.Infof("file %s is empty", filename)
return ReadEmptyFile(options...)
}
if err != nil {
return obiiter.NilIBioSequence, err
}
@@ -305,6 +310,11 @@ func ReadFastaFromStdin(reader io.Reader, options ...WithOption) (obiiter.IBioSe
options = append(options, OptionsSource(obiutils.RemoveAllExt("stdin")))
input, err := Buf(os.Stdin)
if err == ErrNoContent {
log.Infof("stdin is empty")
return ReadEmptyFile(options...)
}
if err != nil {
log.Fatalf("open file error: %v", err)
return obiiter.NilIBioSequence, err

10
pkg/obiformats/fastqseq_read.go
View File

@@ -339,6 +339,11 @@ func ReadFastqFromFile(filename string, options ...WithOption) (obiiter.IBioSequ
file, err := Ropen(filename)
if err == ErrNoContent {
log.Infof("file %s is empty", filename)
return ReadEmptyFile(options...)
}
if err != nil {
return obiiter.NilIBioSequence, err
}
@@ -350,6 +355,11 @@ func ReadFastqFromStdin(reader io.Reader, options ...WithOption) (obiiter.IBioSe
options = append(options, OptionsSource(obiutils.RemoveAllExt("stdin")))
input, err := Buf(os.Stdin)
if err == ErrNoContent {
log.Infof("stdin is empty")
return ReadEmptyFile(options...)
}
if err != nil {
log.Fatalf("open file error: %v", err)
return obiiter.NilIBioSequence, err

19
pkg/obiformats/ngsfilter_read.go
View File

@@ -59,9 +59,13 @@ func _parseMainNGSFilterTags(text string) obingslibrary.TagPair {
}
}
func _parseMainNGSFilter(text string) (obingslibrary.PrimerPair, obingslibrary.TagPair, string, string, bool) {
func _parseMainNGSFilter(text string) (obingslibrary.PrimerPair, obingslibrary.TagPair, string, string, bool, bool) {
fields := strings.Fields(text)
if len(fields) < 6 {
return obingslibrary.PrimerPair{}, obingslibrary.TagPair{}, "", "", false, false
}
tags := _parseMainNGSFilterTags(fields[2])
partial := fields[5] == "T" || fields[5] == "t"
@@ -72,7 +76,8 @@ func _parseMainNGSFilter(text string) (obingslibrary.PrimerPair, obingslibrary.T
tags,
fields[0],
fields[1],
partial
partial,
true
}
func ReadNGSFilter(reader io.Reader) (obingslibrary.NGSLibrary, error) {
@@ -89,7 +94,15 @@ func ReadNGSFilter(reader io.Reader) (obingslibrary.NGSLibrary, error) {
split := strings.SplitN(line, "@", 2)
primers, tags, experiment, sample, partial := _parseMainNGSFilter(split[0])
if len(split) < 1 {
return nil, fmt.Errorf("line %d : invalid format", i+1)
}
primers, tags, experiment, sample, partial, ok := _parseMainNGSFilter(split[0])
if !ok {
return nil, fmt.Errorf("line %d : invalid format", i+1)
}
marker, _ := ngsfilter.GetMarker(primers.Forward, primers.Reverse)
pcr, ok := marker.GetPCR(tags.Forward, tags.Reverse)