Enveomics collection

FastA.mask.rb

Mask sequence region(s) in a FastA file.

    See source code, Artistic license 2.0.

§ References

    Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.

§ Requirements

• Ruby >= 2.0.

§ Usage

FastA.mask.rb --in in_file --out out_file --regions string [opts]

§ Arguments

In*

 --in in_file  Input FastA file.

Out*

 --out out_file  Output FastA file.

Regions*

 --regions string  Regions to mask separated by commas. Each region must be in the format "sequence_id:from..to".

Symbol

 --symbol string  Character used to mask the region(s).

Trim

 --trim   Trim masked regions extending to the edge of a sequence.

Wrap

 --wrap integer  Line length to wrap sequences. Use 0 to generate 1-line sequences.

* Mandatory.