EMBOSS: union

| ## EMBOSS: union

# Program union

## Function

Reads sequence fragments and builds one sequence

## Description

union reads in several sequences, concatenates them and writes them out as a single sequence.

It is most useful when the input sequences are specified in a List file. The List file (file of sequence names) can be any set of sequences in files or database entries specified in the normal EMBOSS USA (which can include the spcification of sub-regions of the sequence, eg. 'em:hsfau[20,55]'). Specifying several such subregions in a sequence or sequences allows you to enter disjoint sequences to be joined.

## Usage

Here is a sample session with union, the file 'cds.list' contains a list of the regions making up the coding sequence of the sequence 'embl:hsfau':

    % union
    Reads sequence fragments and builds one sequence
    Input sequence(s): @cds.list
    Output sequence [hsfau1.fasta]: fau.cds

## Command line arguments

       Mandatory qualifiers:
      [-sequence]          seqall     Sequence database USA
      [-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 database USA | Readable sequence(s) | Required
[-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

The input can be any set of sequences in a file of multiple sequence entries or a List file. The sequences are concatenated in the order in which they appear in the file.

The input used in the above example is:

    em-id:HSFAU1[782:856]
    em-id:HSFAU1[951:1095]
    em-id:HSFAU1[1557:1612]
    em-id:HSFAU1[1787:1912]

You may find the program yank useful for creating List files.

## Output file format

The result if a normal sequence file containnig a single sequence resulting from the concatenation of the input sequences.

## Data files

None.

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
biosed | Replace or delete sequence sections
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 | Writes a list file of the logical OR of two sets of sequences
maskfeat | Mask off features of a sequence
maskseq | Mask off regions of a sequence
newseq | Type in a short new sequence
noreturn | Removes carriage return from ASCII files
notseq | Excludes a set of sequences and writes 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
splitter | Split a sequence into (overlapping) smaller sequences
swissparse | Retrieves sequences from swissprot using keyword search
trimest | Trim poly-A tails off EST sequences
trimseq | Trim ambiguous bits off the ends of sequences
vectorstrip | Strips out DNA between a pair of vector sequences
yank | Reads a sequence range, appends the full USA to a list file

You may find the program yank useful for creating List files.

## Author(s)

This application was written by Peter Rice (peter.rice@uk.lionbioscience.com)

## History

Written (March 2002) - Peter Rice.

## Target users

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

## Comments