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.

It removes the sequence from the specified start to the end positions (inclusive) and returns the rest of the sequence in the output file.

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
   -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.
  [-outseq]            seqout     Output sequence USA

   Optional qualifiers: (none)
   Advanced qualifiers: (none)
   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose


Mandatory qualifiers Allowed values Default
[-sequence]
(Parameter 1)
Sequence USA Readable sequence Required
-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)
[-outseq]
(Parameter 2)
Output sequence USA Writeable sequence <sequence>.format
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

None.

Notes

This can be used as a simple sequence editor.

References

None.

Warnings

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

Diagnostic Error Messages

None.

Exit status

It always exits with status 0

Known bugs

None.

See also

Program nameDescription
biosedReplace or delete sequence sections
degapseqRemoves gap characters from sequences
descseqAlter the name or description of a sequence
entretReads and writes (returns) flatfile entries
extractfeatExtract features from a sequence
extractseqExtract regions from a sequence
listorWrites a list file of the logical OR of two sets of sequences
maskfeatMask off features of a sequence
maskseqMask off regions of a sequence
newseqType in a short new sequence
noreturnRemoves carriage return from ASCII files
notseqExcludes a set of sequences and writes out the remaining ones
nthseqWrites one sequence from a multiple set of sequences
pasteseqInsert one sequence into another
revseqReverse and complement a sequence
seqretReads and writes (returns) sequences
seqretsplitReads and writes (returns) sequences in individual files
splitterSplit a sequence into (overlapping) smaller sequences
swissparseRetrieves sequences from swissprot using keyword search
trimestTrim poly-A tails off EST sequences
trimseqTrim ambiguous bits off the ends of sequences
unionReads sequence fragments and builds one sequence
vectorstripStrips out DNA between a pair of vector sequences
yankReads a sequence range, appends the full USA to a list file

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.

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