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First complete version of obimultiplex2

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Former-commit-id: 170593bd597c7914d3f1fd3d2b865186d7f11966
This commit is contained in:
Eric Coissac
2024-06-06 23:11:13 +02:00
parent 985c91452a
commit 1b43fa4247
9 changed files with 778 additions and 165 deletions
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115
pkg/obiformats/ngsfilter_read.go
View File

@@ -67,24 +67,22 @@ func _parseMainNGSFilterTags(text string) obingslibrary.TagPair {
}
}
func _parseMainNGSFilter(text string) (obingslibrary.PrimerPair, obingslibrary.TagPair, string, string, bool, bool) {
func _parseMainNGSFilter(text string) (obingslibrary.PrimerPair, obingslibrary.TagPair, string, string, bool) {
fields := strings.Fields(text)
if len(fields) != 6 {
return obingslibrary.PrimerPair{}, obingslibrary.TagPair{}, "", "", false, false
return obingslibrary.PrimerPair{}, obingslibrary.TagPair{}, "", "", false
}
tags := _parseMainNGSFilterTags(fields[2])
partial := fields[5] == "T" || fields[5] == "t"
return obingslibrary.PrimerPair{
Forward: fields[3],
Reverse: fields[4],
Forward: strings.ToLower(fields[3]),
Reverse: strings.ToLower(fields[4]),
},
tags,
fields[0],
fields[1],
partial,
true
}
@@ -164,7 +162,12 @@ func OBIMimeNGSFilterTypeGuesser(stream io.Reader) (*mimetype.MIME, io.Reader, e
}
func ReadNGSFilter(reader io.Reader) (*obingslibrary.NGSLibrary, error) {
mimetype, newReader, err := OBIMimeNGSFilterTypeGuesser(reader)
var ngsfilter *obingslibrary.NGSLibrary
var err error
var mimetype *mimetype.MIME
var newReader io.Reader
mimetype, newReader, err = OBIMimeNGSFilterTypeGuesser(reader)
if err != nil {
return nil, err
@@ -172,12 +175,22 @@ func ReadNGSFilter(reader io.Reader) (*obingslibrary.NGSLibrary, error) {
log.Infof("NGSFilter configuration mimetype: %s", mimetype.String())
if mimetype.String() == "text/ngsfilter-csv" {
return ReadCSVNGSFilter(newReader)
if mimetype.String() == "text/ngsfilter-csv" || mimetype.String() == "text/csv" {
ngsfilter, err = ReadCSVNGSFilter(newReader)
} else {
ngsfilter, err = ReadOldNGSFilter(newReader)
}
return ReadOldNGSFilter(newReader)
if err != nil {
return nil, err
}
ngsfilter.CheckPrimerUnicity()
ngsfilter.CheckTagLength()
return ngsfilter, nil
}
func ReadOldNGSFilter(reader io.Reader) (*obingslibrary.NGSLibrary, error) {
ngsfilter := obingslibrary.MakeNGSLibrary()
@@ -196,7 +209,7 @@ func ReadOldNGSFilter(reader io.Reader) (*obingslibrary.NGSLibrary, error) {
return nil, fmt.Errorf("line %d : invalid format", i+1)
}
primers, tags, experiment, sample, partial, ok := _parseMainNGSFilter(split[0])
primers, tags, experiment, sample, ok := _parseMainNGSFilter(split[0])
if !ok {
return nil, fmt.Errorf("line %d : invalid format : \n%s", i+1, line)
@@ -213,7 +226,6 @@ func ReadOldNGSFilter(reader io.Reader) (*obingslibrary.NGSLibrary, error) {
pcr.Experiment = experiment
pcr.Sample = sample
pcr.Partial = partial
if len(split) > 1 && len(split[1]) > 0 {
pcr.Annotations = make(obiseq.Annotation)
@@ -288,9 +300,11 @@ var library_parameter = map[string]func(library *obingslibrary.NGSLibrary, value
case 0:
log.Fatalln("Missing value for @tag_delimiter parameter")
case 1:
library.SetTagDelimiter([]byte(values[0])[0])
value := []byte(values[0])[0]
library.SetTagDelimiter(value)
case 2:
library.SetTagDelimiterFor(values[0], []byte(values[1])[0])
value := []byte(values[1])[0]
library.SetTagDelimiterFor(values[0], value)
default:
log.Fatalln("Invalid value for @tag_delimiter parameter")
}
@@ -300,7 +314,8 @@ var library_parameter = map[string]func(library *obingslibrary.NGSLibrary, value
case 0:
log.Fatalln("Missing value for @forward_tag_delimiter parameter")
case 1:
library.SetForwardTagDelimiter([]byte(values[0])[0])
value := []byte(values[0])[0]
library.SetForwardTagDelimiter(value)
default:
log.Fatalln("Invalid value for @forward_tag_delimiter parameter")
}
@@ -310,7 +325,8 @@ var library_parameter = map[string]func(library *obingslibrary.NGSLibrary, value
case 0:
log.Fatalln("Missing value for @reverse_tag_delimiter parameter")
case 1:
library.SetReverseTagDelimiter([]byte(values[0])[0])
value := []byte(values[0])[0]
library.SetReverseTagDelimiter(value)
default:
log.Fatalln("Invalid value for @reverse_tag_delimiter parameter")
}
@@ -338,21 +354,85 @@ var library_parameter = map[string]func(library *obingslibrary.NGSLibrary, value
log.Fatalf("Invalid value %s for @primer_error parameter", values[0])
}
library.SetAllowedMismatch(dist)
library.SetAllowedMismatches(dist)
case 2:
primer := values[0]
dist, err := strconv.Atoi(values[1])
if err != nil {
log.Fatalf("Invalid value %s for @primer_error parameter", values[1])
}
library.SetAllowedMismatchesFor(primer, dist)
default:
log.Fatalln("Invalid value for @primer_error parameter")
}
},
"forward_mismatches": func(library *obingslibrary.NGSLibrary, values ...string) {
switch len(values) {
case 0:
log.Fatalln("Missing value for @forward_primer_error parameter")
case 1:
dist, err := strconv.Atoi(values[0])
if err != nil {
log.Fatalf("Invalid value %s for @forward_primer_error parameter", values[0])
}
library.SetForwardAllowedMismatches(dist)
default:
log.Fatalln("Invalid value for @forward_primer_error parameter")
}
},
"reverse_mismatches": func(library *obingslibrary.NGSLibrary, values ...string) {
switch len(values) {
case 0:
log.Fatalln("Missing value for @reverse_primer_error parameter")
case 1:
dist, err := strconv.Atoi(values[0])
if err != nil {
log.Fatalf("Invalid value %s for @reverse_primer_error parameter", values[0])
}
library.SetReverseAllowedMismatches(dist)
default:
log.Fatalln("Invalid value for @reverse_primer_error parameter")
}
},
"indels": func(library *obingslibrary.NGSLibrary, values ...string) {
switch len(values) {
case 0:
log.Fatalln("Missing value for @indels parameter")
case 1:
library.SetAllowsIndels(values[0] == "true")
case 2:
library.SetAllowsIndelsFor(values[0], values[1] == "true")
default:
log.Fatalln("Invalid value for @indels parameter")
}
},
"forward_indels": func(library *obingslibrary.NGSLibrary, values ...string) {
switch len(values) {
case 0:
log.Fatalln("Missing value for @forward_indels parameter")
case 1:
library.SetForwardAllowsIndels(values[0] == "true")
default:
log.Fatalln("Invalid value for @forward_indels parameter")
}
},
"reverse_indels": func(library *obingslibrary.NGSLibrary, values ...string) {
switch len(values) {
case 0:
log.Fatalln("Missing value for @reverse_indels parameter")
case 1:
library.SetReverseAllowsIndels(values[0] == "true")
default:
log.Fatalln("Invalid value for @reverse_indels parameter")
}
},
}
func ReadCSVNGSFilter(reader io.Reader) (*obingslibrary.NGSLibrary, error) {
@@ -451,7 +531,6 @@ func ReadCSVNGSFilter(reader io.Reader) (*obingslibrary.NGSLibrary, error) {
pcr.Experiment = fields[experimentColIndex]
pcr.Sample = fields[sampleColIndex]
pcr.Partial = false
if extraColumns != nil {
pcr.Annotations = make(obiseq.Annotation)

2
pkg/obiformats/universal_read.go
View File

@@ -43,7 +43,7 @@ func OBIMimeTypeGuesser(stream io.Reader) (*mimetype.MIME, io.Reader, error) {
}
fastqDetector := func(raw []byte, limit uint32) bool {
ok, err := regexp.Match("^@[^ ]", raw)
ok, err := regexp.Match("^@[^ ].*\n[^ ]+\n\\+", raw)
return ok && err == nil
}