
                               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
