
                                  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 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 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 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 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

   Standard (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

   Additional (Optional) qualifiers (* if not always prompted):
   -tolower            toggle     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 (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 standard output
   -filter              boolean    Read standard input, write 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 deaths


   Standard (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
   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. A 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

   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

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
