
                              EMBOSS: abiview
     _________________________________________________________________
   
                                Program abiview
                                       
Function

   Reads ABI file and display the trace
   
Description

   abiview reads in an ABI sequence trace file and graphically displays
   the results.
   
   The data for each nucleotide is plotted and the assigned nucleotide
   (G, A, T, C or N) in the ABI file is overlayed on the graphs.
   
   It also writes out the sequence to an output sequence file.
   
Usage

   Here is a sample session with abiview:

% abiview
Name of the ABI trace file: ba16d2.s1
Output sequence [outfile.fasta]:
Graph type [x11]:

Command line arguments

   Mandatory qualifiers:
  [-fname]             string     Name of the ABI trace file
  [-outseq]            seqout     Sequence file
   -graph              xygraph    Graph type

   Optional qualifiers:
   -yticks             bool       Display y-axis ticks
   -[no]sequence       bool       Display the sequence on the graph
   -window             integer    Sequence display window size
   -bases              string     Base graphs to be displayed

   Advanced qualifiers:
   -separate           bool       Separate the trace graphs for the 4 bases

   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
   [-fname]
   (Parameter 1) Name of the ABI trace file Any string is accepted An
   empty string is accepted
   [-outseq]
   (Parameter 2) Sequence file Writeable sequence <sequence>.format
   -graph Graph type EMBOSS has a list of known devices, including
   postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows,
   x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm,
   png EMBOSS_GRAPHICS value, or x11
   Optional qualifiers Allowed values Default
   -yticks Display y-axis ticks Yes/No No
   -[no]sequence Display the sequence on the graph Yes/No Yes
   -window Sequence display window size Any integer value 40
   -bases Base graphs to be displayed Any string is accepted GATC
   Advanced qualifiers Allowed values Default
   -separate Separate the trace graphs for the 4 bases Yes/No No
   
Input file format

   This reads in a standard ABI trace file.
   
Output file format

   It outputs a file holding a normal nucleotide sequence.
   
   It outputs a graphical image of the traces.
   The graphical output from the above example is here.
   
   The horizontal scale of the output image labelled 'Residue Position'
   is only a very approximate indication of the spacing of residues in
   the image. The real residue spacing is variable, as it relies on the
   speed with which the oligo-nucleotides are eluted in the ABI
   sequencer. Do not be surprised to see the nucleotide signals spaced at
   a much greater distance than the horizontal scale might suggest.
   
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
   cirdna Draws circular maps of DNA constructs
   lindna Draws linear maps of DNA constructs
   pepnet Displays proteins as a helical net
   pepwheel Shows protein sequences as helices
   prettyplot Displays aligned sequences, with colouring and boxing
   prettyseq Output sequence with translated ranges
   remap Display a sequence with restriction cut sites, translation etc
   seealso Finds programs sharing group names
   showalign Displays a multiple sequence alignment
   showdb Displays information on the currently available databases
   showfeat Show features of a sequence
   showseq Display a sequence with features, translation etc
   textsearch Search sequence documentation text. SRS and Entrez are
   faster!
   
Author(s)

   This application was written by Tim Carver (tcarver@hgmp.mrc.ac.uk)
   
History

   Written (January 2001) - Tim Carver
   
Target users

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