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

   Optional qualifiers: (none)
   Advanced qualifiers: (none)
   General qualifiers:
  -help                boolean    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
[-insseq]
(Parameter 2)
Sequence to insert Readable sequence Required
-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)
[-outseq]
(Parameter 3)
Output sequence USA Writeable sequence <sequence>.format
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

None.

Notes

This can be used as a simple sequence editor.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program nameDescription
biosedReplace or delete sequence sections
cutseqRemoves a specified section from a sequence
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
revseqReverse and complement a sequence
seqretReads and writes (returns) sequences
seqretsplitReads and writes (returns) sequences in individual files
skipseqReads and writes (returns) sequences, skipping the first few
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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