maskseq
Function
Description
This simple editing program allows you to mask off regions of a
sequence with a specified letter.
Why would you wish to do this? It is common for database
searches to mask out low-complexity or biased composition
regions of a sequence so that spurious matches do not occur.
It is just possible that you have a program that has reported
such biased regions but which has not masked the sequence
itself. In that case, you can use this program to do the
masking.
You may find other uses for it.
Some non-EMBOSS programs (for example FASTA) are capable of treating
lower-case regions as if they are masked. maskseq can mask a
region to lower-case instead of replacing the sequence with 'N's or 'X's
if you use the qualifier '-tolower' or use a space character as the
masking character.
Usage
Command line arguments
Input file format
maskseq reads in a single sequence USA.
You can specify a file of ranges to mask out by giving the '-regions'
qualifier the value '@' followed by the name of the file containing the
ranges. (eg: '-regions @myfile').
The format of the range file is:
- Comment lines start with '#' in the first column.
- Comment lines and blank lines are ignored.
- The line may start with white-space.
- There are two positive (integer) numbers per line separated by one or
more space or TAB characters.
- The second number must be greater or equal to the first number.
- There can be optional text after the two numbers to annotate the line.
- White-space before or after the text is removed.
An example range file is:
# this is my set of ranges
12 23
4 5 this is like 12-23, but smaller
67 10348 interesting region
Output file format
maskseq writes s single masked sequence file.
Data files
None.
Notes
None.
References
None.
Warnings
You can mask out a complete sequence.
Diagnostic Error Messages
Several warning messages about malformed region specifications:
- Non-digit found in region ...
- Unpaired start of a region found in ...
- Non-digit found in region ...
- The start of a pair of region positions must be smaller than the
end in ...
Exit status
It exits with status 0, unless a region is badly constructed.
Known bugs
None.
Author(s)
History
Target users
Comments