EMBOSS: cutseq


Program cutseq

Function

Removes a specified section from a sequence

Description

This simple editing program allows you to cut out a region from your sequence by specifying the begin and end positions of the sequence to remove.

Usage

To remove bases 10 to 12 from a sequence 'gatta.seq' and write to the new sequence file 'gatta2.seq':
% cutseq gatta.seq gatta2.seq -from=10 -to=12

To remove the first 20 bases from 'hatta.seq' and write it to 'jsh.seq':

% cutseq -seq=hatta.seq -from=1 -to=20 -out=jsh.seq

Command line arguments

   Mandatory qualifiers:
  [-sequence]          sequence   Sequence USA
  [-outseq]            seqout     Output sequence USA
   -from               integer    This is the start position (inclusive) of
                                  the section of the sequence that you wish to
                                  remove.
   -to                 integer    This is the end position (inclusive) of the
                                  section of the sequence that you wish to
                                  remove.

   Optional qualifiers: (none)
   Advanced qualifiers: (none)

Mandatory qualifiers Allowed values Default
[-sequence]
(Parameter 1)
Sequence USA Readable sequence Required
[-outseq]
(Parameter 2)
Output sequence USA Writeable sequence <sequence>.format
-from This is the start position (inclusive) of the section of the sequence that you wish to remove. Any integer value Start of sequence (0)
-to This is the end position (inclusive) of the section of the sequence that you wish to remove. Any integer value End of sequence (0)
Optional qualifiers Allowed values Default
(none)
Advanced qualifiers Allowed values Default
(none)

Input file format

Single sequence.

Output file format

Single sequence file.

Data files

Notes

This can be used as a simple sequence editor.

References

Warnings

You can delete a complete sequence and write out an empty sequence file.

Diagnostic Error Messages

Exit status

It always exits with status 0

Known bugs

Bugs noted but not yet fixed.

None.

See also

Program nameDescription
descseqAlter the name or description of a sequence
extractseqExtract regions from a sequence
maskfeatMask off features of a sequence
maskseqMask off regions of a sequence
megamergerMerge two large overlapping nucleic acid sequences
mergerMerge two overlapping nucleic acid sequences
newseqType in a short new sequence
noreturnRemoves carriage return from ASCII files
nthseqWrites one sequence from a multiple set of sequences
pasteseqInsert one sequence into another
revseqReverse and complement a sequence
splitterSplit a sequence into (overlapping) smaller sequences
trimseqTrim ambiguous bits off the ends of sequences
vectorstripStrips out DNA between a pair of vector sequences

Author(s)

This application was written by Gary Williams (gwilliam@hgmp.mrc.ac.uk)

History

Completed 26 Jan 1999

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments