FastA.extract.rb
Extracts a list of sequences and/or coordinates from multi-FastA files.
See source code, Artistic license 2.0.
§ References
Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.
§ Requirements
§ Usage
FastA.extract.rb --in in_file --out out_file [opts]
§ Arguments
- Input file*
--in in_fileInput FastA file.- Output file*
--out out_fileOutput FastA file.- Coordinates
--coords stringComma-delimited list of coordinates (mandatory unless -C is passed). The format of the coordinates is SEQ:FROM..TO or SEQ:FROM~LEN: SEQ: Sequence ID, or * (asterisk) to extract range from all sequences FROM: Integer, position of the first base to include (can be negative) TO: Integer, last base to include (can be negative) LEN: Length of the range to extract.- Coordinates file
--coords-file in_fileFile containing the coordinates, one per line. Each line must follow the format described for Coordinates.- Quiet
--quietRun quietly (no STDERR output).