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
|
acdtrace
Function
ACD compiler on-screen trace
Description
Acdtrace reports the processing of lines in an ACD file, including the
resolution of any variables or ACD functions.
Acdtrace does not have its own command line. Instead, it will run the
command line of any EMBOSS program by reading its ACD file and
processing the command line and user responses in exactly the same way
as the true program.
Acdtrace uses a very simple method. The first command line parameter
is the name of the EMBOSS program to be compiled. All other command
line parameters and qualifiers are processed by that program's ACD
file.
Usage
Here is a sample session with acdtrace
% acdtrace antigenic
Finds antigenic sites in proteins
Input protein sequence(s): tsw:actb1_fugru
Minimum length of antigenic region [6]:
Output report [actb1_fugru.antigenic]:
Go to the input files for this example
Go to the output files for this example
Command line arguments
The first parameter is the name of the program to compile. All other
command line parameters and qualifiers are defined for that program -
see the documentation for the program of choice.
Output file format
The output file is empty, but any format available to the specified
program can be used.
Output files for usage example
File: actb1_fugru.antigenic
Data files
Acdtrace will use any data files specified in the ACD file of the
specified program, but will ignore any data files that are only used
directly by the program's code.
EMBOSS data files are distributed with the application and stored in
the standard EMBOSS data directory, which is defined by the EMBOSS
environment variable EMBOSS_DATA.
To see the available EMBOSS data files, run:
% embossdata -showall
To fetch one of the data files (for example 'Exxx.dat') into your
current directory for you to inspect or modify, run:
% embossdata -fetch -file Exxx.dat
Users can provide their own data files in their own directories.
Project specific files can be put in the current directory, or for
tidier directory listings in a subdirectory called ".embossdata".
Files for all EMBOSS runs can be put in the user's home directory, or
again in a subdirectory called ".embossdata".
The directories are searched in the following order:
* . (your current directory)
* .embossdata (under your current directory)
* ~/ (your home directory)
* ~/.embossdata
Notes
References
Warnings
None.
Diagnostic Error Messages
Exit status
It exits with status 0.
Known bugs
None.
See also
Program name Description
acdc ACD compiler
acdpretty ACD pretty printing utility
acdtable Creates an HTML table from an ACD file
acdvalid ACD file validation
Author(s)
Peter Rice (pmr ebi.ac.uk)
Informatics Division, European Bioinformatics Institute, Wellcome
Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
History
Target users
This program is intended to be used by developers of applications and
interfaces.
Comments
None
|
