                                   maskseq



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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

Write a sequence with masked regions
Version: EMBOSS:6.2.0

   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 and exit. 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
   -version            boolean    Report version number and exit


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
   nthseqset        Reads and writes (returns) one set of sequences from many
   pasteseq         Insert one sequence into another
   revseq           Reverse and complement a nucleotide sequence
   seqret           Reads and writes (returns) sequences
   seqretsetall     Reads and writes (returns) many sets of 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
   splitsource      Split sequence(s) into original source sequences
   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 (c) 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
