
                              EMBOSS: maskseq
     _________________________________________________________________
   
                                Program maskseq
                                       
Function

   Mask off regions of a sequence
   
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.
   
Usage

   To mask off bases 10 to 12 from a sequence 'gatta.seq' and write to
   the new sequence file 'gatta2.seq':
   
% maskseq gatta.seq gatta2.seq -reg=10-12

   To mask off bases 20 to 30 from a sequence 'hdh.seq' using the
   character 'n' and write to the new sequence file 'hdh2.seq':
   
% maskseq hdh.seq hdh2.seq -reg=20-30 -mask=n

   To mask off the regions 20 to 23, 34 to 45 and 88 to 90 in 'yuy.seq':
   
% maskseq yuy.seq yuy2.seq -reg=20-23,34-45,88-90

Command line arguments

   Mandatory qualifiers:
  [-sequence]          sequence   Sequence USA
   -regions            range      Regions to mask.
                                  A set of regions is specified by a set of
                                  pairs of positions.
                                  The positions are integers.
                                  They are separated by any non-digit,
                                  non-alpha character.
                                  Examples of region specifications are:
                                  24-45, 56-78
                                  1:45, 67=99;765..888
                                  1,5,8,10,23,45,57,99
  [-outseq]            seqout     Output sequence USA

   Optional qualifiers:
   -maskchar           string     Character to use when masking.
                                  Default is 'X' for protein sequences, 'N'
                                  for nucleic sequences.

   Advanced qualifiers: (none)
   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   Mandatory qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) Sequence USA Readable sequence Required
   -regions Regions to mask. A set of regions is specified by a set of
   pairs of positions. The positions are integers. They are separated by
   any non-digit, non-alpha character. Examples of region specifications
   are: 24-45, 56-78 1:45, 67=99;765..888 1,5,8,10,23,45,57,99 Sequence
   range None
   [-outseq]
   (Parameter 2) Output sequence USA Writeable sequence <sequence>.format
   Optional qualifiers Allowed values Default
   -maskchar Character to use when masking. Default is 'X' for protein
   sequences, 'N' for nucleic sequences. Any string is accepted 'X' for
   protein, 'N' for nucleic
   Advanced qualifiers Allowed values Default
   (none)
   
Input file format

   This program reads in a single sequence file.
   
   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

   Single 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.
   
See also

   Program name                          Description
   biosed       Replace or delete sequence sections
   cutseq       Removes a specified section from a sequence
   degapseq     Removes gap characters from sequences
   descseq      Alter the name or description of a sequence
   entret       Reads and writes (returns) flatfile entries
   extractfeat  Extract features from a sequence
   extractseq   Extract regions from a sequence
   listor       Writes a list file of the logical OR of two sets of sequences
   maskfeat     Mask off features of a sequence
   newseq       Type in a short new sequence
   noreturn     Removes carriage return from ASCII files
   notseq       Excludes a set of sequences and writes out the remaining ones
   nthseq       Writes one sequence from a multiple set of sequences
   pasteseq     Insert one sequence into another
   revseq       Reverse and complement a sequence
   seqret       Reads and writes (returns) sequences
   seqretsplit  Reads and writes (returns) sequences in individual files
   splitter     Split a sequence into (overlapping) smaller sequences
   swissparse   Retrieves sequences from swissprot using keyword search
   trimest      Trim poly-A tails off EST sequences
   trimseq      Trim ambiguous bits off the ends of sequences
   union        Reads sequence fragments and builds one sequence
   vectorstrip  Strips out DNA between a pair of vector sequences
   yank         Reads a sequence range, appends the full USA to a list file
   
   maskfeat masks parts of the input sequence that are annotated features
   whose feature-names match the user-specified names.
   
Author(s)

   This application was written by Gary Williams
   (gwilliam@hgmp.mrc.ac.uk)
   
History

   Completed 3 March 1999
   
Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.
   
Comments
