| 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.

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

Here is a sample session with maskseq

Mask off bases 10 to 12 from a sequence 'prot.fasta' and write to the new sequence file 'prot2.seq':

    % maskseq ../../data/prot.fasta prot2.seq -reg=10-12
    Mask off regions of a sequence.

Go to the input files for this example
Go to the output files for this example

Example 2

Mask off bases 20 to 30 from a sequence 'prot.fasta' using the character 'x' and write to the new sequence file 'prot2.seq':

    % maskseq ../../data/prot.fasta prot2.seq -reg=20-30 -mask=x
    Mask off regions of a sequence.

Go to the output files for this example

Example 3

Mask off the regions 20 to 23, 34 to 45 and 88 to 90 in 'prot.fasta':

    % maskseq ../../data/prot.fasta prot2.seq -reg=20-23,34-45,88-90
    Mask off regions of a sequence.

Go to the output files for this example

Example 4

Change to lower-case the regions 20 to 23, 34 to 45 and 88 to 90 in 'prot.fasta':

    % maskseq ../../data/prot.fasta prot2.seq -reg=20-23,34-45,88-90 -tolower
    Mask off regions of a sequence.

Go to the output files for this example

## 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 (* if not always prompted):
       -tolower            boolean    The region can be 'masked' by converting the
                                      sequence characters to lower-case, some
                                      non-EMBOSS programs e.g. fasta can interpret
                                      this as a masked region. The sequence is
                                      unchanged apart from the case change. You
                                      might like to ensure that the whole sequence
                                      is in upper-case before masking the
                                      specified regions to lower-case by using the
                                      '-supper' flag.
    *  -maskchar           string     Character to use when masking.
                                      Default is 'X' for protein sequences, 'N'
                                      for nucleic sequences.
                                      If the mask character is set to be the SPACE
                                      character or a null character, then the
                                      sequence is 'masked' by changing it to
                                      lower-case, just as with the '-lowercase'
                                      flag.

       Advanced qualifiers: (none)
       Associated qualifiers:
      "-sequence" related qualifiers
       -sbegin1             integer    First base used
       -send1               integer    Last base used, def=seq length
       -sreverse1           boolean    Reverse (if DNA)
       -sask1               boolean    Ask for begin/end/reverse
       -snucleotide1        boolean    Sequence is nucleotide
       -sprotein1           boolean    Sequence is protein
       -slower1             boolean    Make lower case
       -supper1             boolean    Make upper case
       -sformat1            string     Input sequence format
       -sopenfile1          string     Input filename
       -sdbname1            string     Database name
       -sid1                string     Entryname
       -ufo1                string     UFO features
       -fformat1            string     Features format
       -fopenfile1          string     Features file name
      "-outseq" related qualifiers
       -osformat2           string     Output seq format
       -osextension2        string     File name extension
       -osname2             string     Base file name
       -osdirectory2        string     Output directory
       -osdbname2           string     Database name to add
       -ossingle2           boolean    Separate file for each entry
       -oufo2               string     UFO features
       -offormat2           string     Features format
       -ofname2             string     Features file name
       -ofdirectory2        string     Output directory

       General qualifiers:
       -auto                boolean    Turn off prompts
       -stdout              boolean    Write standard output
       -filter              boolean    Read standard input, write standard output
       -options             boolean    Prompt for required and optional values
       -debug               boolean    Write debug output to program.dbg
       -acdlog              boolean    Write ACD processing log to program.acdlog
       -acdpretty           boolean    Rewrite ACD file as program.acdpretty
       -acdtable            boolean    Write HTML table of options
       -verbose             boolean    Report some/full command line options
       -help                boolean    Report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning             boolean    Report warnings
       -error               boolean    Report errors
       -fatal               boolean    Report fatal errors
       -die                 boolean    Report deaths

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
-tolower | The region can be 'masked' by converting the sequence characters to lower-case, some non-EMBOSS programs e.g. fasta can interpret this as a masked region. The sequence is unchanged apart from the case change. You might like to ensure that the whole sequence is in upper-case before masking the specified regions to lower-case by using the '-supper' flag. | Boolean value Yes/No | No
-maskchar | Character to use when masking. Default is 'X' for protein sequences, 'N' for nucleic sequences. If the mask character is set to be the SPACE character or a null character, then the sequence is 'masked' by changing it to lower-case, just as with the '-lowercase' flag. | Any string is accepted | 'X' for protein, 'N' for nucleic
Advanced qualifiers | Allowed values | Default
(none)

## Input file format

maskseq reads in a single sequence USA.

### Input files for usage example

### File: ../../data/prot.fasta

    >FASTA F00001 FASTA FORMAT PROTEIN SEQUENCE
    ACDEFGHIKLMNPQRSTVWY
    ACDEFGHIKLMNPQRSTVWY
    ACDEFGHIKLMNPQRSTVWY
    ACDEFGHIKLMNPQRSTVWY
    ACDEFGHIKLMNPQRSTVWY

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.

### Output files for usage example

### File: prot2.seq

    >FASTA F00001 FASTA FORMAT PROTEIN SEQUENCE
    ACDEFGHIKXXXPQRSTVWYACDEFGHIKLMNPQRSTVWYACDEFGHIKLMNPQRSTVWY
    ACDEFGHIKLMNPQRSTVWYACDEFGHIKLMNPQRSTVWY

### Output files for usage example 2

### File: prot2.seq

    >FASTA F00001 FASTA FORMAT PROTEIN SEQUENCE
    ACDEFGHIKLMNPQRSTVWxxxxxxxxxxxMNPQRSTVWYACDEFGHIKLMNPQRSTVWY
    ACDEFGHIKLMNPQRSTVWYACDEFGHIKLMNPQRSTVWY

### Output files for usage example 3

### File: prot2.seq

    >FASTA F00001 FASTA FORMAT PROTEIN SEQUENCE
    ACDEFGHIKLMNPQRSTVWXXXXEFGHIKLMNPXXXXXXXXXXXXGHIKLMNPQRSTVWY
    ACDEFGHIKLMNPQRSTVWYACDEFGHXXXMNPQRSTVWY

### Output files for usage example 4

### File: prot2.seq

    >FASTA F00001 FASTA FORMAT PROTEIN SEQUENCE
    ACDEFGHIKLMNPQRSTVWyacdEFGHIKLMNPqrstvwyacdefGHIKLMNPQRSTVWY
    ACDEFGHIKLMNPQRSTVWYACDEFGHiklMNPQRSTVWY

## 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
skipseq | Reads and writes (returns) sequences, skipping the first few
splitter | Split a sequence into (overlapping) smaller sequences
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)

Gary Williams (gwilliam © hgmp.mrc.ac.uk)
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, 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