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maskseq |
Function
Mask off regions of a sequenceDescription
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 maskseqMask 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 |
| codcopy | Reads and writes a codon usage table |
| 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 | Write 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 | Exclude a set of sequences and write 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 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