
                                  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 -graph cps 
Reads ABI file and display the trace
ABI trace file: abiview.abi
Output sequence [abiview.fasta]: 

Created abiview.ps

   Go to the input files for this example
   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-infile]            infile     ABI trace file
  [-outseq]            seqout     Output sequence USA
   -graph              xygraph    Graph type

   Additional (Optional) qualifiers:
   -startbase          integer    First base to report or display
   -endbase            integer    Last sequence base to report or display. If
                                  the default is set to zero then the value of
                                  this is taken as the maximum number of
                                  bases.
   -yticks             boolean    Display y-axis ticks
   -[no]sequence       boolean    Display the sequence on the graph
   -window             integer    Sequence display window size
   -bases              string     Base graphs to be displayed

   Advanced (Unprompted) qualifiers:
   -separate           boolean    Separate the trace graphs for the 4 bases

   Associated qualifiers:

   "-outseq" associated qualifiers
   -osformat2           string     Output seq format
   -osextension2        string     File name extension
   -osname2             string     Base file name
   -osdirectory2        string     Output directory
   -osdbname2           string     Database name to add
   -ossingle2           boolean    Separate file for each entry
   -oufo2               string     UFO features
   -offormat2           string     Features format
   -ofname2             string     Features file name
   -ofdirectory2        string     Output directory

   "-graph" associated qualifiers
   -gprompt             boolean    Graph prompting
   -gtitle              string     Graph title
   -gsubtitle           string     Graph subtitle
   -gxtitle             string     Graph x axis title
   -gytitle             string     Graph y axis title
   -goutfile            string     Output file for non interactive displays
   -gdirectory          string     Output directory

   General qualifiers:
   -auto                boolean    Turn off prompts
   -stdout              boolean    Write standard output
   -filter              boolean    Read standard input, write standard output
   -options             boolean    Prompt for standard and additional values
   -debug               boolean    Write debug output to program.dbg
   -verbose             boolean    Report some/full command line options
   -help                boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning             boolean    Report warnings
   -error               boolean    Report errors
   -fatal               boolean    Report fatal errors
   -die                 boolean    Report deaths


   Standard (Mandatory) qualifiers Allowed values Default
   [-infile]
   (Parameter 1) ABI trace file Input file Required
   [-outseq]
   (Parameter 2) Output sequence USA 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, xml EMBOSS_GRAPHICS value, or x11
   Additional (Optional) qualifiers Allowed values Default
   -startbase First base to report or display Integer 0 or more 0
   -endbase Last sequence base to report or display. If the default is
   set to zero then the value of this is taken as the maximum number of
   bases. Any integer value 0
   -yticks Display y-axis ticks Boolean value Yes/No No
   -[no]sequence Display the sequence on the graph Boolean value Yes/No
   Yes
   -window Sequence display window size Any integer value 40
   -bases Base graphs to be displayed Any string is accepted, matching
   regular expression /[GATC]+/ GATC
   Advanced (Unprompted) qualifiers Allowed values Default
   -separate Separate the trace graphs for the 4 bases Boolean value
   Yes/No No

Input file format

   This reads in a standard ABI trace file.

  Input files for usage example

  File: abiview.abi

   This file contains non-printing characters and so cannot be displayed
   here.

  File: abiview.abi

   This file contains non-printing characters and so cannot be displayed
   here.

Output file format

   It outputs a file holding a normal nucleotide sequence.

  Output files for usage example

  File: abiview.fasta

>../../data/abiview.abi
GNNNNNNNNNGNGNNGGGGTTTNANNNTNNNAGAACCCCCCTTNGAAAANNNCCACCCCA
NNATAGTNGTANGAATAGTNCCCAGGCCANGCCTATCTGTGATGATTACATAGGCTAACA
CATGACAAACATTTAAAAACACTAAACAATTGTTATTTATTCTTTGTTCCTATAAACCAC
ACCCATTAAGCCCTTACTATATATAAGAGTTTTCAAGCCAAGAACCTGCTGCTTGGGAGG
CTGATGCAGGAGAATTGCCAAGTACAAACCCTGCCTGGACTGTAAAGTGAAACCAAGGCT
AGTTGTCTCACAATAAAAGATGAAGGGCAAGTGGGATCAATGCATAAAGGAGCTTGTGCC
CAAGCCTGTTAGCCTTAGTTCAATTCCTGAGTACCATGAAAAGGTAGAAGGAGAGAAATG
ATTTGGTACAATTTTTCTCTGTGCTGTGACACAGTACCACCCTCCTACTAATAACAAATA
AAATAATGTTTAAAACAAAATAAAATAAAAATGGACTGGGATGTAGCACAATGGTAGGGT
ACTTGCATAGCATGTACAAGGACCTGATTTCAATCCCCTGTGATAAAAGAAAATAAGGAA
GGGAGGAAGCGTTAGGAGGAAAAATGGAATACAGAAGACACAGTGCATGGGAAGGATATG
TATGTTATGAACACCAGAAATTCACTTGAAAATGAGTAAAATTTTTTTATTATTATATCA
TTATTATTGGGGGGGATGTGGGCGGGGCTTGCAGAGGTATCTTTTAGAGGANGATCATTT
TCCGGTTGTTGAGCAGGGCTCTGTTATGTAGGATATCTCAGANTAACAGACCCCAGGT

  Graphics File: abiview.ps

   [abiview results]

   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
   sixpack Display a DNA sequence with 6-frame translation and ORFs
   textsearch Search sequence documentation text. SRS and Entrez are
   faster!

Author(s)

   Tim Carver (tcarver © rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, 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

   None
