-
Notifications
You must be signed in to change notification settings - Fork 0
/
abiview.html
447 lines (347 loc) · 11.1 KB
/
abiview.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
<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>