move the worker class to the obiseq package

pkg/obitools/obiannotate/options.go

@@ -0,0 +1,93 @@
+package obiannotate
+
+import (
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obigrep"
+	"github.com/DavidGamba/go-getoptions"
+)
+
+var _addRank = false
+var _toBeRenamed = make(map[string]string, 0)
+var _toBeDeleted = make([]string, 0)
+var _keepOnly = make([]string, 0)
+var _taxonAtRank = make([]string, 0)
+var _tagList = ""
+var _clearAll = false
+var _setSeqLength = false
+var _uniqueID = false
+
+func SequenceSelectionOptionSet(options *getoptions.GetOpt) {
+	options.BoolVar(&_addRank, "seq-rank", _addRank,
+		options.Description("Adds a new attribute named seq_rank to the sequence record indicating its entry number in the sequence file."),
+	)
+
+	options.BoolVar(&_clearAll, "clear", _clearAll,
+		options.Alias("C"),
+		options.Description("Clears all attributes associated to the sequence records."),
+	)
+
+	options.BoolVar(&_setSeqLength, "length", _setSeqLength,
+		options.Description("Adds attribute with seq_length as a key and sequence length as a value."),
+	)
+
+	options.BoolVar(&_uniqueID, "uniq-id", _uniqueID,
+		options.Description("Forces sequence record ids to be unique."),
+	)
+	options.StringMapVar(&_toBeRenamed, "rename-tag", 1, 1,
+		options.Alias("R"),
+		options.ArgName("NEW_NAME=OLD_NAME"),
+		options.Description("Changes attribute name <OLD_NAME> to <NEW_NAME>. When attribute named <OLD_NAME>"+
+			" is missing, the sequence record is skipped and the next one is examined."))
+
+	options.StringSliceVar(&_toBeDeleted, "delete-tag", 1, 1,
+		options.ArgName("KEY"),
+		options.Description(" Deletes attribute named <KEY>.When this attribute is missing,"+
+			" the sequence record is skipped and the next one is examined."))
+
+	options.StringSliceVar(&_taxonAtRank, "with-taxon-at-rank", 1, 1,
+		options.ArgName("RANK_NAME"),
+		options.Description("Adds taxonomic annotation at taxonomic rank <RANK_NAME>."))
+
+	options.StringVar(&_tagList, "tag-list", _tagList,
+		options.ArgName("FILENAME"),
+		options.Description("<FILENAME> points to a file containing attribute names"+
+			" and values to modify for specified sequence records."))
+
+	options.StringSliceVar(&_keepOnly, "keep", 1, 1,
+		options.Alias("k"),
+		options.ArgName("KEY"),
+		options.Description("Keeps only attribute with key <KEY>. Several -k options can be combined."))
+
+}
+
+// OptionSet adds to the basic option set every options declared for
+// the obipcr command
+func OptionSet(options *getoptions.GetOpt) {
+	obiconvert.OptionSet(options)
+	obigrep.SequenceSelectionOptionSet(options)
+	SequenceSelectionOptionSet(options)
+}
+
+// -S <KEY>:<PYTHON_EXPRESSION>, --set-tag=<KEY>:<PYTHON_EXPRESSION>
+// Creates a new attribute named with a key <KEY> and a value computed from <PYTHON_EXPRESSION>.
+
+// --set-identifier=<PYTHON_EXPRESSION>
+// Sets sequence record identifier with a value computed from <PYTHON_EXPRESSION>.
+
+// --run=<PYTHON_EXPRESSION>
+// Runs a python expression on each selected sequence.
+
+// --set-sequence=<PYTHON_EXPRESSION>
+// Changes the sequence itself with a value computed from <PYTHON_EXPRESSION>.
+
+// -T, --set-definition=<PYTHON_EXPRESSION>
+// Sets sequence definition with a value computed from <PYTHON_EXPRESSION>.
+
+// -O, --only-valid-python
+// Allows only valid python expressions.
+
+// -m <MCLFILE>, --mcl=<MCLFILE>
+// Creates a new attribute containing the number of the cluster the sequence record was assigned to, as indicated in file <MCLFILE>.
+
+// --uniq-id
+// Forces sequence record ids to be unique.