EMBOSS: pasteseq


Program pasteseq

Function

Insert one sequence into another

Description

This simple editing program allows you to insert one sequence into another sequence after a specified position and to then write out the results to a sequence file.

Usage

To insert the sequence 'tst.seq' after position 67 in sequence 'ese.seq' and write the results to the file 'estste.seq':
% pasteseq ese.seq tst.seq estste.seq -pos=67

This is probably slightly more readable if the argument names are used instead of relying on the parameter positions:

% pasteseq -seq=ese.seq -ins=tst.seq -out=estste.seq -pos=67

To insert the sequence 'tst.seq' before the start of sequence 'ese.seq' use -pos=0 :

% pasteseq -seq=ese.seq -ins=tst.seq -out=estste.seq -pos=0

Command line arguments

   Mandatory qualifiers:
  [-sequence]          sequence   Sequence USA
  [-insseq]            sequence   Sequence to insert
  [-outseq]            seqout     Output sequence USA
   -pos                integer    The position in the main input sequence to
                                  insert after.
                                  To insert before the start use the position
                                  0.

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

Mandatory qualifiers Allowed values Default
[-sequence]
(Parameter 1)
Sequence USA Readable sequence Required
[-insseq]
(Parameter 2)
Sequence to insert Readable sequence Required
[-outseq]
(Parameter 3)
Output sequence USA Writeable sequence <sequence>.format
-pos The position in the main input sequence to insert after. To insert before the start use the position 0. Integer 0 or more $(sequence.end)
Optional qualifiers Allowed values Default
(none)
Advanced qualifiers Allowed values Default
(none)

Input file format

The sequence and the sequence to insert into it are both single sequence.

Output file format

Single sequence file.

Data files

Notes

This can be used as a simple sequence editor.

References

Warnings

Diagnostic Error Messages

Exit status

It always exits with status 0.

Known bugs

Bugs noted but not yet fixed.

None.

See also

Program nameDescription
cutseqRemoves a specified section from a sequence
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
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