                                   abiview



Wiki

   The master copies of EMBOSS documentation are available at
   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

Function

   Display the trace in an ABI sequencer file

Description

   abiview reads in an ABI sequencer trace file and graphically displays
   the data. The probabilities of each of the 4 nucleotide bases along the
   sequencing run is plotted and the assigned nucleotide (G, A, T, C or N)
   from the ABI file is overlayed on the graphs. The complete sequence is
   written to an output file.

Usage

   Here is a sample session with abiview


% abiview -graph cps
Display the trace in an ABI sequencer file
ABI sequencing trace file: abiview.abi
nucleotide 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

Display the trace in an ABI sequencer file
Version: EMBOSS:6.5.6.0

   Standard (Mandatory) qualifiers:
  [-infile]            infile     ABI sequencing trace file
  [-outseq]            seqout     [.] Nucleotide sequence
                                  filename and optional format (output USA)
   -graph              xygraph    [$EMBOSS_GRAPHICS value, or x11] Graph type
                                  (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                  tek, tekt, none, data, xterm, png, gif, pdf,
                                  svg)

   Additional (Optional) qualifiers:
   -startbase          integer    [0] First base to report or display (Integer
                                  0 or more)
   -endbase            integer    [0] 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)
   -yticks             boolean    [N] Display y-axis ticks
   -[no]sequence       boolean    [Y] Display the sequence on the graph
   -window             integer    [40] Sequence display window size (Any
                                  integer value)
   -bases              string     [GATC] Base graphs to be displayed (Any
                                  string, matching regular expression
                                  /[GATC]+/)

   Advanced (Unprompted) qualifiers:
   -separate           boolean    [N] 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
   -gdesc              string     Graph description
   -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 first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 and exit. 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 dying program messages
   -version            boolean    Report version number and exit


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

>abiview
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

   An ABI file (*.abi) contains sequence trace data and base calls from a
   run of an ABI nucleotide sequencer machine. A trace data file is what
   you get back from having some DNA sequenced, for example, by a 3730XL
   sequencer. The files are in "binary" format and so cannot be viewed
   directly on screen. To inspect the sequencing data you must use a trace
   viewer such as abiview. Another good trace viewer is FinchTV
   (http://www.geospiza.com/finchtv/). It is a stand-alone program and is
   freely available.

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       Draw circular map of DNA constructs
                   coderet      Extract CDS, mRNA and translations from feature tables
                   entret       Retrieve sequence entries from flatfile databases and files
  extractalign     Extract regions from a sequence alignment
                   iep          Calculate the isoelectric point of proteins
                   infoalign    Display basic information about a multiple sequence alignment
                   infoseq      Display basic information about sequences
                   lindna       Draw linear maps of DNA constructs
                   pepinfo      Plot amino acid properties of a protein sequence in parallel
                   pepnet       Draw a helical net for a protein sequence
                   pepwheel     Draw a helical wheel diagram for a protein sequence
                   plotorf      Plot potential open reading frames in a nucleotide sequence
                   prettyplot   Draw a sequence alignment with pretty formatting
                   prettyseq    Write a nucleotide sequence and its translation to file
                   refseqget    Get reference sequence
                   remap        Display restriction enzyme binding sites in a nucleotide sequence
                   seqxref      Retrieve all database cross-references for a sequence entry
                   seqxrefget   Retrieve all cross-referenced data for a sequence entry
                   showalign    Display a multiple sequence alignment in pretty format
                   showfeat     Display features of a sequence in pretty format
                   showpep      Display protein sequences with features in pretty format
                   sixpack      Display a DNA sequence with 6-frame translation and ORFs
  variationget     Get sequence variations
                   whichdb      Search all sequence databases for an entry and retrieve it

Author(s)

   Tim              Carver formerly at:
   MRC              Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome           Campus, Hinxton, Cambridge, CB10 1SB, UK

                    Please report all bugs to the EMBOSS bug team
                    (emboss-bug (c) emboss.open-bio.org) not to the original author.

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
