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<HTML>
<HEAD>
<TITLE>
EMBOSS: abiview
</TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">
<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
abiview
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Reads ABI file and display the trace
<H2>
Description
</H2>
<b>abiview</b> reads in an ABI sequence trace file and graphically
displays the results.
<p>
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.
<p>
It also writes out the sequence to an output sequence file.
<H2>
Usage
</H2>
<b>Here is a sample session with abiview</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>abiview -graph cps </b>
Reads ABI file and display the trace
ABI sequencing trace file: <b>abiview.abi</b>
nucleotide output sequence [abiview.fasta]: <b></b>
Created abiview.ps
</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><a href="#output.1">Go to the output files for this example</a><p><p>
<H2>
Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
Standard (Mandatory) qualifiers:
[-infile] infile ABI sequencing trace file
[-outseq] seqout [<sequence>.<format>] Nucleotide sequence
filename and optional format (output USA)
-graph xygraph [$EMBOSS_GRAPHICS value, or x11] Graph type
(ps, hpgl, hp7470, hp7580, meta, cps, x11,
tekt, tek, none, data, xterm, png, gif)
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 is accepted, 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 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 dying program messages
</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Standard (Mandatory) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>[-infile]<br>(Parameter 1)</td>
<td>ABI sequencing trace file</td>
<td>Input file</td>
<td><b>Required</b></td>
</tr>
<tr>
<td>[-outseq]<br>(Parameter 2)</td>
<td>Nucleotide sequence filename and optional format (output USA)</td>
<td>Writeable sequence</td>
<td><i><*></i>.<i>format</i></td>
</tr>
<tr>
<td>-graph</td>
<td>Graph type</td>
<td>EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tekt, tek, none, data, xterm, png, gif</td>
<td><i>EMBOSS_GRAPHICS</i> value, or x11</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Additional (Optional) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>-startbase</td>
<td>First base to report or display</td>
<td>Integer 0 or more</td>
<td>0</td>
</tr>
<tr>
<td>-endbase</td>
<td>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.</td>
<td>Any integer value</td>
<td>0</td>
</tr>
<tr>
<td>-yticks</td>
<td>Display y-axis ticks</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>
<tr>
<td>-[no]sequence</td>
<td>Display the sequence on the graph</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>
<tr>
<td>-window</td>
<td>Sequence display window size</td>
<td>Any integer value</td>
<td>40</td>
</tr>
<tr>
<td>-bases</td>
<td>Base graphs to be displayed</td>
<td>Any string is accepted, matching regular expression /[GATC]+/</td>
<td>GATC</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Advanced (Unprompted) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>-separate</td>
<td>Separate the trace graphs for the 4 bases</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>
</table>
<H2>
Input file format
</H2>
This reads in a standard ABI trace file.
<p>
<a name="input.1"></a>
<h3>Input files for usage example </h3>
<p><h3>File: abiview.abi</h3>
<p>This file contains non-printing characters and so cannot be displayed here.
<p><h3>File: abiview.abi</h3>
<p>This file contains non-printing characters and so cannot be displayed here.
<H2>
Output file format
</H2>
It outputs a file holding a normal nucleotide sequence.
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: abiview.fasta</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
>../../data/abiview.abi
GNNNNNNNNNGNGNNGGGGTTTNANNNTNNNAGAACCCCCCTTNGAAAANNNCCACCCCA
NNATAGTNGTANGAATAGTNCCCAGGCCANGCCTATCTGTGATGATTACATAGGCTAACA
CATGACAAACATTTAAAAACACTAAACAATTGTTATTTATTCTTTGTTCCTATAAACCAC
ACCCATTAAGCCCTTACTATATATAAGAGTTTTCAAGCCAAGAACCTGCTGCTTGGGAGG
CTGATGCAGGAGAATTGCCAAGTACAAACCCTGCCTGGACTGTAAAGTGAAACCAAGGCT
AGTTGTCTCACAATAAAAGATGAAGGGCAAGTGGGATCAATGCATAAAGGAGCTTGTGCC
CAAGCCTGTTAGCCTTAGTTCAATTCCTGAGTACCATGAAAAGGTAGAAGGAGAGAAATG
ATTTGGTACAATTTTTCTCTGTGCTGTGACACAGTACCACCCTCCTACTAATAACAAATA
AAATAATGTTTAAAACAAAATAAAATAAAAATGGACTGGGATGTAGCACAATGGTAGGGT
ACTTGCATAGCATGTACAAGGACCTGATTTCAATCCCCTGTGATAAAAGAAAATAAGGAA
GGGAGGAAGCGTTAGGAGGAAAAATGGAATACAGAAGACACAGTGCATGGGAAGGATATG
TATGTTATGAACACCAGAAATTCACTTGAAAATGAGTAAAATTTTTTTATTATTATATCA
TTATTATTGGGGGGGATGTGGGCGGGGCTTGCAGAGGTATCTTTTAGAGGANGATCATTT
TCCGGTTGTTGAGCAGGGCTCTGTTATGTAGGATATCTCAGANTAACAGACCCCAGGT
</pre>
</td></tr></table><p>
<p><h3>Graphics File: abiview.ps</h3>
<p><img src="abiview.1.abiview.gif" alt="[abiview results]">
<p>
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.
<H2>
Data files
</H2>
None.
<H2>
Notes
</H2>
None.
<H2>
References
</H2>
None.
<H2>
Warnings
</H2>
None.
<H2>
Diagnostic Error Messages
</H2>
None.
<H2>
Exit status
</H2>
It always exits with status 0.
<H2>
Known bugs
</H2>
None.
<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th><th>Description</th></tr>
<tr>
<td><a href="cirdna.html">cirdna</a></td>
<td>Draws circular maps of DNA constructs</td>
</tr>
<tr>
<td><a href="lindna.html">lindna</a></td>
<td>Draws linear maps of DNA constructs</td>
</tr>
<tr>
<td><a href="pepnet.html">pepnet</a></td>
<td>Displays proteins as a helical net</td>
</tr>
<tr>
<td><a href="pepwheel.html">pepwheel</a></td>
<td>Shows protein sequences as helices</td>
</tr>
<tr>
<td><a href="prettyplot.html">prettyplot</a></td>
<td>Displays aligned sequences, with colouring and boxing</td>
</tr>
<tr>
<td><a href="prettyseq.html">prettyseq</a></td>
<td>Output sequence with translated ranges</td>
</tr>
<tr>
<td><a href="remap.html">remap</a></td>
<td>Display sequence with restriction sites, translation etc</td>
</tr>
<tr>
<td><a href="seealso.html">seealso</a></td>
<td>Finds programs sharing group names</td>
</tr>
<tr>
<td><a href="showalign.html">showalign</a></td>
<td>Displays a multiple sequence alignment</td>
</tr>
<tr>
<td><a href="showdb.html">showdb</a></td>
<td>Displays information on the currently available databases</td>
</tr>
<tr>
<td><a href="showfeat.html">showfeat</a></td>
<td>Show features of a sequence</td>
</tr>
<tr>
<td><a href="showseq.html">showseq</a></td>
<td>Display a sequence with features, translation etc</td>
</tr>
<tr>
<td><a href="sixpack.html">sixpack</a></td>
<td>Display a DNA sequence with 6-frame translation and ORFs</td>
</tr>
<tr>
<td><a href="textsearch.html">textsearch</a></td>
<td>Search sequence documentation. Slow, use SRS and Entrez!</td>
</tr>
</table>
<H2>
Author(s)
</H2>
Tim Carver (tcarver © rfcgr.mrc.ac.uk)
<br>
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
<H2>
History
</H2>
Written (January 2001) - Tim Carver
<H2>
Target users
</H2>
This program is intended to be used by everyone and everything, from naive users to embedded scripts.
<H2>
Comments
</H2>
None
</BODY>
</HTML>
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