transliterate_seq

Biopiece: transliterate_seq

Description

Transliteration is ultra fast search and replace (or search and delete) of characters in sequence and is useful for things as lowercasing sequence, converting sequence from RNA to DNA or convering soft-masked sequence to hard-masked.

Usage

... | transliterate_seq [options]

Options

[-?          | --help]               #  Print full usage description.
[-s <string> | --search=<string>]    #  String of chars to locate and replace
[-r <string> | --replace=<string>]   #  String of chars for replacing
[-d <string> | --delete=<string>]    #  String of chars to delete
[-I <file!>  | --stream_in=<file!>]  #  Read input from stream file  -  Default=STDIN
[-O <file>   | --stream_out=<file>]  #  Write output to stream file  -  Default=STDOUT
[-v          | --verbose]            #  Verbose output.

Examples

To lowercase sequence:

transliterate_seq -s ATCGUN -r atcgun

To convert RNA to DNA:

transliterate_seq -s Uu -r Tt

To convert soft-masked sequence to hard-masked:

transliterate_seq -s atcgu -r NNNNN

To remove all N's from a sequence:

transliterate_seq -s nN -d

See also

transliterate_vals

uppercase_seq

Author

Martin Asser Hansen - Copyright (C) - All rights reserved.

mail@maasha.dk

August 2007

License

GNU General Public License version 2

http://www.gnu.org/copyleft/gpl.html

Help

transliterate_seq is part of the Biopieces framework.

http://www.biopieces.org