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111 lines
3.1 KiB
Go
111 lines
3.1 KiB
Go
package obipcr
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import (
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log "github.com/sirupsen/logrus"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiapat"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
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"github.com/DavidGamba/go-getoptions"
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)
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var _Circular = false
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var _ForwardPrimer string
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var _ReversePrimer string
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var _AllowedMismatch = 0
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var _MinimumLength = 0
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var _MaximumLength = -1
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// PCROptionSet defines every options related to a simulated PCR.
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//
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// The function adds to a CLI every options proposed to the user
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// to tune the parametters of the PCR simulation algorithm.
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//
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// Parameters
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//
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// - option : is a pointer to a getoptions.GetOpt instance normaly
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// produced by the
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func PCROptionSet(options *getoptions.GetOpt) {
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options.BoolVar(&_Circular, "circular", false,
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options.Alias("c"),
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options.Description("Considers that sequences are [c]ircular."))
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options.StringVar(&_ForwardPrimer, "forward", "",
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options.Required("You must provide a forward primer"),
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options.Description("The forward primer used for the electronic PCR."))
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options.StringVar(&_ReversePrimer, "reverse", "",
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options.Required("You must provide a reverse primer"),
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options.Description("The reverse primer used for the electronic PCR."))
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options.IntVar(&_AllowedMismatch, "allowed-mismatches", 0,
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options.Alias("e"),
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options.Description("Maximum number of mismatches allowed for each primer."))
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options.IntVar(&_MinimumLength, "min-length", 0,
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options.Alias("l"),
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options.Description("Minimum length of the barcode (primers excluded)."))
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options.IntVar(&_MaximumLength, "max-length", -1,
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options.Alias("L"),
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options.Description("Maximum length of the barcode (primers excluded)."))
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}
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// OptionSet adds to the basic option set every options declared for
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// the obipcr command
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func OptionSet(options *getoptions.GetOpt) {
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obiconvert.OptionSet(options)
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PCROptionSet(options)
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}
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// ForwardPrimer returns the sequence of the forward primer as indicated by the
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// --forward command line option
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func ForwardPrimer() string {
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pattern, err := obiapat.MakeApatPattern(_ForwardPrimer, _AllowedMismatch, false)
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if err != nil {
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log.Fatalf("%+v", err)
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}
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pattern.Free()
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return _ForwardPrimer
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}
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// ReversePrimer returns the sequence of the reverse primer as indicated by the
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// --reverse command line option
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func ReversePrimer() string {
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pattern, err := obiapat.MakeApatPattern(_ReversePrimer, _AllowedMismatch,false)
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if err != nil {
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log.Fatalf("%+v", err)
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}
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pattern.Free()
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return _ReversePrimer
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}
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// AllowedMismatch returns the allowed mistmatch count between each
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// primer and the sequences as indicated by the
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// --allowed-mismatches|-e command line option
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func AllowedMismatch() int {
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return _AllowedMismatch
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}
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// Circular returns the considered sequence topology as indicated by the
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// --circular|-c command line option
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func Circular() bool {
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return _Circular
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}
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// MinLength returns the amplicon minimum length as indicated by the
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// --min-length|-l command line option
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func MinLength() int {
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return _MinimumLength
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}
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// MaxLength returns the amplicon maximum length as indicated by the
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// --max-length|-L command line option
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func MaxLength() int {
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return _MaximumLength
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}
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