Task Name: extract-sequence
Extracts annotated regions from an input sequence.
Parameters:
in — semicolon-separated list of input files. [String, Required]
out — output file. [String, Required]
annotation-names — list of annotations names which will be accepted or filtered. [String, Required]
accept-or-filter — if set to true, accepts only the specified annotations, if set to false, accepts all annotations except the specified ones. [Boolean, Optional]
complement — complements the annotated regions if the corresponding annotation is located on the complement strand. [Boolean, Optional]
extend-left — extends the resulting regions to the left for the specified number of base symbols. [Number, Optional]
extend-right — extends the resulting regions to the right for the specified number of base symbols. [Number, Optional]
gap-length — inserts a gap of the specified length between the merged annotations.
transl - translates the annotated regions. [Boolean, Optional]
Example:
ugene extract-sequence --in=sars.gb --out=res.fa --annotation-names=gene