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Add option related to agrep match on obigrep and obiannotate

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This commit is contained in:
Eric Coissac
2024-09-09 16:52:13 +02:00
parent 65ae82622e
commit 05bf2bfd6c
12 changed files with 167 additions and 34 deletions
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60
pkg/obitools/obigrep/options.go
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@@ -6,6 +6,7 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiapat"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats/ncbitaxdump"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
@@ -43,6 +44,11 @@ var _SaveRejected = ""
var _PairedMode = "forward"
var _approx_pattern = make([]string, 0)
var _pattern_error = 0
var _pattern_indel = false
var _pattern_only_forward = false
func TaxonomySelectionOptionSet(options *getoptions.GetOpt) {
options.StringVar(&_Taxdump, "taxdump", _Taxdump,
@@ -143,6 +149,23 @@ func SequenceSelectionOptionSet(options *getoptions.GetOpt) {
options.Description("If paired reads are passed to obibrep, that option determines how the conditions "+
"are applied to both reads."),
)
options.StringSliceVar(&_approx_pattern, "approx-pattern", 1, 1,
options.ArgName("PATTERN"),
options.Description("Regular expression pattern to be tested against the sequence itself. The pattern is case insensitive."))
options.IntVar(&_pattern_error, "pattern-error", _pattern_error,
options.Description("Maximum number of allowed error during pattern matching"),
)
options.BoolVar(&_pattern_indel, "allows-indels", _pattern_indel,
options.Description("Allows for indel during pattern matching"),
)
options.BoolVar(&_pattern_only_forward, "only-forward", _pattern_only_forward,
options.Description("Look for pattern only on forward strand"),
)
}
// OptionSet adds to the basic option set every options declared for
@@ -212,6 +235,18 @@ func CLISelectedNCBITaxDump() string {
return _Taxdump
}
func CLIPatternError() int {
return _pattern_error
}
func CLIPatternInDels() bool {
return _pattern_indel
}
func CLIPatternBothStrand() bool {
return !_pattern_only_forward
}
func CLILoadSelectedTaxonomy() *obitax.Taxonomy {
if CLISelectedNCBITaxDump() != "" {
if _Taxonomy == nil {
@@ -327,6 +362,30 @@ func CLISequencePatternPredicate() obiseq.SequencePredicate {
return nil
}
func CLISequenceAgrep() obiseq.SequencePredicate {
if len(_approx_pattern) > 0 {
p := obiapat.IsPatternMatchSequence(
_approx_pattern[0],
CLIPatternError(),
CLIPatternBothStrand(),
CLIPatternInDels(),
)
for _, pattern := range _approx_pattern[1:] {
p = p.And(obiapat.IsPatternMatchSequence(
pattern,
CLIPatternError(),
CLIPatternBothStrand(),
CLIPatternInDels(),
))
}
return p
}
return nil
}
func CLIDefinitionPatternPredicate() obiseq.SequencePredicate {
if len(_DefinitionPatterns) > 0 {
@@ -419,6 +478,7 @@ func CLISequenceSelectionPredicate() obiseq.SequencePredicate {
p = p.And(CLIIdListPredicate())
p = p.And(CLIHasAttibutePredicate())
p = p.And(CLIIsAttibuteMatchPredicate())
p = p.And(CLISequenceAgrep())
if _InvertMatch {
p = p.Not()