obitools/obitools4
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Xprize update

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Former-commit-id: d38919a897961e4d40da3b844057c3fb94fdb6d7
This commit is contained in:
Eric Coissac
2024-07-25 18:09:03 -04:00
parent 4e4fac491f
commit 67665a6b40
18 changed files with 895 additions and 29 deletions
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30
pkg/obitools/obiannotate/obiannotate.go
View File

@@ -215,6 +215,24 @@ func AddTaxonAtRankWorker(taxonomy *obitax.Taxonomy, ranks ...string) obiseq.Seq
return f
}
func AddTaxonRankWorker(taxonomy *obitax.Taxonomy) obiseq.SeqWorker {
f := func(s *obiseq.BioSequence) (obiseq.BioSequenceSlice, error) {
taxonomy.SetTaxonomicRank(s)
return obiseq.BioSequenceSlice{s}, nil
}
return f
}
func AddScientificNameWorker(taxonomy *obitax.Taxonomy) obiseq.SeqWorker {
f := func(s *obiseq.BioSequence) (obiseq.BioSequenceSlice, error) {
taxonomy.SetScientificName(s)
return obiseq.BioSequenceSlice{s}, nil
}
return f
}
func AddSeqLengthWorker() obiseq.SeqWorker {
f := func(s *obiseq.BioSequence) (obiseq.BioSequenceSlice, error) {
s.SetAttribute("seq_length", s.Len())
@@ -266,6 +284,18 @@ func CLIAnnotationWorker() obiseq.SeqWorker {
annotator = annotator.ChainWorkers(w)
}
if CLISetTaxonomicRank() {
taxo := obigrep.CLILoadSelectedTaxonomy()
w := AddTaxonRankWorker(taxo)
annotator = annotator.ChainWorkers(w)
}
if CLISetScientificName() {
taxo := obigrep.CLILoadSelectedTaxonomy()
w := AddScientificNameWorker(taxo)
annotator = annotator.ChainWorkers(w)
}
if CLIHasAddLCA() {
taxo := obigrep.CLILoadSelectedTaxonomy()
w := obitax.AddLCAWorker(taxo, CLILCASlotName(), CLILCAThreshold())

16
pkg/obitools/obiannotate/options.go
View File

@@ -32,6 +32,8 @@ var _lcaError = 0.0
var _setId = ""
var _cut = ""
var _taxonomicPath = false
var _withRank = false
var _withScientificName = false
func SequenceAnnotationOptionSet(options *getoptions.GetOpt) {
// options.BoolVar(&_addRank, "seq-rank", _addRank,
@@ -117,6 +119,12 @@ func SequenceAnnotationOptionSet(options *getoptions.GetOpt) {
options.BoolVar(&_taxonomicPath, "taxonomic-path", _taxonomicPath,
options.Description("Annotate the sequence with its taxonomic path"))
options.BoolVar(&_withRank, "taxonomic-rank", _withRank,
options.Description("Annotate the sequence with its taxonomic rank"))
options.BoolVar(&_withScientificName, "scientific-name", _withScientificName,
options.Description("Annotate the sequence with its scientific name"))
// options.StringVar(&_tagList, "tag-list", _tagList,
// options.ArgName("FILENAME"),
// options.Description("<FILENAME> points to a file containing attribute names"+
@@ -307,3 +315,11 @@ func CLIPatternInDels() bool {
func CLISetTaxonomicPath() bool {
return _taxonomicPath
}
func CLISetTaxonomicRank() bool {
return _withRank
}
func CLISetScientificName() bool {
return _withScientificName
}