| maskseq

## Function

Write a sequence with masked regions

## Description

maskseq reads a sequence and writes a masked version of it to file. The sequence is masked in a specified set of regions such that characters in that region are (optionally) converted to lower case and / or (optionally) replaced with the specified mask 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 prot.fasta prot2.seq -reg=10-12
    Write a sequence with masked regions

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 prot.fasta prot2.seq -reg=20-30 -mask=x
    Write a sequence with masked regions

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 prot.fasta prot2.seq -reg=20-23,34-45,88-90
    Write a sequence with masked regions

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 prot.fasta prot2.seq -reg=20-23,34-45,88-90 -tolower
    Write a sequence with masked regions

Go to the output files for this example

## Command line arguments

       Standard (Mandatory) qualifiers:
      [-sequence]          sequence   Sequence filename and optional format, or
                                      reference (input USA)
       -regions            range      [None] 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     [.] Sequence filename and
                                      optional format (output USA)

       Additional (Optional) qualifiers (* if not always prompted):
       -tolower            toggle     [N] 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     ['X' for protein, 'N' for nucleic] 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 from 1 to 1 characters)

       Advanced (Unprompted) qualifiers: (none)
       Associated qualifiers:

       "-sequence" associated qualifiers
       -sbegin1            integer    Start of the sequence to be used
       -send1              integer    End of the sequence to be used
       -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
       -sdbname1           string     Database name
       -sid1               string     Entryname
       -ufo1               string     UFO features
       -fformat1           string     Features format
       -fopenfile1         string     Features file name

       "-outseq" associated 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 first file to standard output
       -filter             boolean    Read first file from standard input, write
                                      first file to standard output
       -options            boolean    Prompt for standard and additional values
       -debug              boolean    Write debug output to program.dbg
       -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 dying program messages

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Sequence filename and optional format, or reference (input 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) | Sequence filename and optional format (output USA) | Writeable sequence | <*>.format
Additional (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. | Toggle 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 from 1 to 1 characters | 'X' for protein, 'N' for nucleic
Advanced (Unprompted) qualifiers | Allowed values | Default
(none)

## Input file format

maskseq reads in a single sequence USA.

### Input files for usage example

### File: 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

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 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.

There are other uses for it. For example, 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.

## 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
--- | ---
aligncopy | Reads and writes alignments
aligncopypair | Reads and writes pairs from alignments
biosed | Replace or delete sequence sections
codcopy | Copy and reformat a codon usage table
cutseq | Removes a section from a sequence
degapseq | Removes non-alphabetic (e.g. gap) characters from sequences
descseq | Alter the name or description of a sequence
entret | Retrieves sequence entries from flatfile databases and files
extractalign | Extract regions from a sequence alignment
extractfeat | Extract features from sequence(s)
extractseq | Extract regions from a sequence
featcopy | Reads and writes a feature table
featreport | Reads and writes a feature table
listor | Write a list file of the logical OR of two sets of sequences
makenucseq | Create random nucleotide sequences
makeprotseq | Create random protein sequences
maskambignuc | Masks all ambiguity characters in nucleotide sequences with N
maskambigprot | Masks all ambiguity characters in protein sequences with X
maskfeat | Write a sequence with masked features
newseq | Create a sequence file from a typed-in sequence
nohtml | Remove mark-up (e.g. HTML tags) from an ASCII text file
noreturn | Remove carriage return from ASCII files
nospace | Remove all whitespace from an ASCII text file
notab | Replace tabs with spaces in an ASCII text file
notseq | Write to file a subset of an input stream of sequences
nthseq | Write to file a single sequence from an input stream of sequences
pasteseq | Insert one sequence into another
revseq | Reverse and complement a nucleotide sequence
seqret | Reads and writes (returns) sequences
seqretsplit | Reads sequences and writes them to individual files
sizeseq | Sort sequences by size
skipredundant | Remove redundant sequences from an input set
skipseq | Reads and writes (returns) sequences, skipping first few
splitter | Split sequence(s) into smaller sequences
trimest | Remove poly-A tails from nucleotide sequences
trimseq | Remove unwanted characters from start and end of sequence(s)
trimspace | Remove extra whitespace from an ASCII text file
union | Concatenate multiple sequences into a single sequence
vectorstrip | Removes vectors from the ends of nucleotide sequence(s)
yank | Add a sequence reference (a full USA) to a list file

## Author(s)

Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust 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

None