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CANADA: clean_out

clean_out (version 1.0)

This program reads nucleic acid sequences, removes all whitespaces and other characters
not encoding bases, and writes the clean sequences to standard output.The sequences are
usually read from an input file. If no filename is given, clean_out works in interactive mode.
In this mode the user is prompted to type in a sequence, and the clean sequence is put out
immediately. You can leave the interactive mode (and exit the program) by entering @.

See the manual for a more detailed description of this tool.

Download

The program:    clean_out.exe (248 KB)

Example

An interactive sequence cleaning tolerating degenerate bases could look like this:

>clean_out -iupac
Enter sequence (@ to exit):
acgatcgac
acgatcgac

Enter sequence (@ to exit):
abcdefghijklmnopqrstuvwxyz
abcdghkmrstuvwy

Enter sequence (@ to exit):
@
last modification: Jun/20/2007

  
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