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comparison GEMBASSY-1.0.3/doc/text/gdnawalk.txt @ 0:8300eb051bea draft

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1 gdnawalk
2 Function
3
4 Draws DNA Walk map of the genome
5
6 Description
7
8 gdnawalk draws the DNA Walk map of the given genome. DNA Walk is drawn by
9 moving a single pixel per nucleotide, in the direction specified for each
10 base. Here A is moved upward, T downward, G to the right, and C to the
11 left. Position zero (first letter of the genome) is indicated by the
12 crossing of thin axes.
13
14 G-language SOAP service is provided by the
15 Institute for Advanced Biosciences, Keio University.
16 The original web service is located at the following URL:
17
18 http://www.g-language.org/wiki/soap
19
20 WSDL(RPC/Encoded) file is located at:
21
22 http://soap.g-language.org/g-language.wsdl
23
24 Documentation on G-language Genome Analysis Environment methods are
25 provided at the Document Center
26
27 http://ws.g-language.org/gdoc/
28
29 Usage
30
31 Here is a sample session with gdnawalk
32
33 % gdnawalk refseqn:NC_000913
34 Draws DNA Walk map of the genome
35 Created gdnawalk.1.png
36
37 Go to the input files for this example
38 Go to the output files for this example
39
40 Command line arguments
41
42 Standard (Mandatory) qualifiers:
43 [-sequence] seqall Nucleotide sequence(s) filename and optional
44 format, or reference (input USA)
45
46 Additional (Optional) qualifiers: (none)
47 Advanced (Unprompted) qualifiers:
48 -format string [png] Output file format. Dependent on
49 'convert' command (Any string)
50 -goutfile string [gdnawalk] Output file for non interactive
51 displays (Any string)
52
53 Associated qualifiers:
54
55 "-sequence" associated qualifiers
56 -sbegin1 integer Start of each sequence to be used
57 -send1 integer End of each sequence to be used
58 -sreverse1 boolean Reverse (if DNA)
59 -sask1 boolean Ask for begin/end/reverse
60 -snucleotide1 boolean Sequence is nucleotide
61 -sprotein1 boolean Sequence is protein
62 -slower1 boolean Make lower case
63 -supper1 boolean Make upper case
64 -scircular1 boolean Sequence is circular
65 -sformat1 string Input sequence format
66 -iquery1 string Input query fields or ID list
67 -ioffset1 integer Input start position offset
68 -sdbname1 string Database name
69 -sid1 string Entryname
70 -ufo1 string UFO features
71 -fformat1 string Features format
72 -fopenfile1 string Features file name
73
74 General qualifiers:
75 -auto boolean Turn off prompts
76 -stdout boolean Write first file to standard output
77 -filter boolean Read first file from standard input, write
78 first file to standard output
79 -options boolean Prompt for standard and additional values
80 -debug boolean Write debug output to program.dbg
81 -verbose boolean Report some/full command line options
82 -help boolean Report command line options and exit. More
83 information on associated and general
84 qualifiers can be found with -help -verbose
85 -warning boolean Report warnings
86 -error boolean Report errors
87 -fatal boolean Report fatal errors
88 -die boolean Report dying program messages
89 -version boolean Report version number and exit
90
91 Input file format
92
93 The database definitions for following commands are available at
94 http://soap.g-language.org/kbws/embossrc
95
96 gdnawalk reads one or more nucleotide sequences.
97
98 Output file format
99
100 The output from gdnawalk is to an image file.
101
102
103
104 Data files
105
106 None.
107
108 Notes
109
110 None.
111
112 References
113
114 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
115 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
116 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
117
118 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
119 large-scale analysis of high-throughput omics data, J. Pest Sci.,
120 31, 7.
121
122 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
123 Analysis Environment with REST and SOAP Web Service Interfaces,
124 Nucleic Acids Res., 38, W700-W705.
125
126 Warnings
127
128 None.
129
130 Diagnostic Error Messages
131
132 None.
133
134 Exit status
135
136 It always exits with a status of 0.
137
138 Known bugs
139
140 None.
141
142 See also
143
144 gcircularmap Draws circular map of the genome
145 ggenomemap3 Draws the map of the genome (version 3)
146
147 Author(s)
148
149 Hidetoshi Itaya (celery@g-language.org)
150 Institute for Advanced Biosciences, Keio University
151 252-0882 Japan
152
153 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
154 Institute for Advanced Biosciences, Keio University
155 252-0882 Japan
156
157 History
158
159 2012 - Written by Hidetoshi Itaya
160 2013 - Fixed by Hidetoshi Itaya
161
162 Target users
163
164 This program is intended to be used by everyone and everything, from
165 naive users to embedded scripts.
166
167 Comments
168
169 None.
170