biosed
Function
Description
biosed is a simple sequence editing utility that searches for a
target subsequence in one or more input sequences and replaces it with a
specified second subsequence (or optionally just deletes the found
target subsequence).
biosed was inspired by the useful UNIX utility sed which
searches for a pattern in text and can replace or delete the found
pattern.
If the target subsequence occurs more than once, then each instance of
the target is replaced.
The target subsequence is not any sort of an ambiguity pattern, it is
just a short sequence. A simple string match is done and if it exactly
matches then the replacement is done. The matching is independent of
the case of the sequence or the target - both uppercase and lowercase
will match.
Usage
Command line arguments
Input file format
It reads the USA of one or more nucleic acid or protein sequences.
Output file format
The edited sequence is output.
The sequence will be in uppercase.
Data files
None.
Notes
The edited sequence will be output in uppercase.
References
None.
Warnings
No check is made on the replacement subsequence.
Any text can be used as the replacement, including characters only used
in proteins (e.g. D, E, F, etc.), characters not used in proteins (e.g.
J, O, etc), digits and punctuation characters.
Diagnostic Error Messages
None.
Exit status
Author(s)
History
Target users
Comments