EMBOSS: abiview

| abiview

## Wiki

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## 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

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
[-infile] (Parameter 1) | infile | ABI sequencing trace file | Input file | Required
[-outseq] (Parameter 2) | seqout | Nucleotide sequence filename and optional format (output USA) | Writeable sequence | <*>.format
-graph | xygraph | Graph type | EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, pdf, svg | EMBOSS_GRAPHICS value, or x11
Additional (Optional) qualifiers
-startbase | integer | First base to report or display | Integer 0 or more | 0
-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. | Any integer value | 0
-yticks | boolean | Display y-axis ticks | Boolean value Yes/No | No
-[no]sequence | boolean | Display the sequence on the graph | Boolean value Yes/No | Yes
-window | integer | Sequence display window size | Any integer value | 40
-bases | string | Base graphs to be displayed | Any string, matching regular expression /[GATC]+/ | GATC
Advanced (Unprompted) qualifiers
-separate | boolean | Separate the trace graphs for the 4 bases | Boolean value Yes/No | No
Associated qualifiers
"-outseq" associated seqout qualifiers
-osformat2 -osformat_outseq | string | Output seq format | Any string |
-osextension2 -osextension_outseq | string | File name extension | Any string |
-osname2 -osname_outseq | string | Base file name | Any string |
-osdirectory2 -osdirectory_outseq | string | Output directory | Any string |
-osdbname2 -osdbname_outseq | string | Database name to add | Any string |
-ossingle2 -ossingle_outseq | boolean | Separate file for each entry | Boolean value Yes/No | N
-oufo2 -oufo_outseq | string | UFO features | Any string |
-offormat2 -offormat_outseq | string | Features format | Any string |
-ofname2 -ofname_outseq | string | Features file name | Any string |
-ofdirectory2 -ofdirectory_outseq | string | Output directory | Any string |
"-graph" associated xygraph qualifiers
-gprompt | boolean | Graph prompting | Boolean value Yes/No | N
-gdesc | string | Graph description | Any string |
-gtitle | string | Graph title | Any string |
-gsubtitle | string | Graph subtitle | Any string |
-gxtitle | string | Graph x axis title | Any string | Residue Position
-gytitle | string | Graph y axis title | Any string |
-goutfile | string | Output file for non interactive displays | Any string |
-gdirectory | string | Output directory | Any string |
General qualifiers
-auto | boolean | Turn off prompts | Boolean value Yes/No | N
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N
-warning | boolean | Report warnings | Boolean value Yes/No | Y
-error | boolean | Report errors | Boolean value Yes/No | Y
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y
-die | boolean | Report dying program messages | Boolean value Yes/No | Y
-version | boolean | Report version number and exit | Boolean value Yes/No | N

## 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

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 © 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