Mercurial > repos > ktnyt > gembassy

comparison GEMBASSY-1.0.3/doc/text/ggenomemap3.txt @ 0:8300eb051bea draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Initial upload
author ktnyt
date Fri, 26 Jun 2015 05:19:29 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:8300eb051bea
1 ggenomemap3
2 Function
3
4 Draws the map of the genome (version 3)
5
6 Description
7
8 ggenomemap3 creates a map of the genome, showing the local nucleotide
9 contents and positions of genes. A is shown in red, T is shown in green,
10 G is shown in yellow, and C is shown in blue.
11 Created image has a resolution of 8192x8192 and is suited for conversion
12 to SVG, which can be performed by specifying the -format option. The formats
13 available are dependent to the "convert" command from ImageMagick.
14
15 G-language SOAP service is provided by the
16 Institute for Advanced Biosciences, Keio University.
17 The original web service is located at the following URL:
18
19 http://www.g-language.org/wiki/soap
20
21 WSDL(RPC/Encoded) file is located at:
22
23 http://soap.g-language.org/g-language.wsdl
24
25 Documentation on G-language Genome Analysis Environment methods are
26 provided at the Document Center
27
28 http://ws.g-language.org/gdoc/
29
30 Usage
31
32 Here is a sample session with ggenomemap3
33
34 % ggenomemap3 refseqn:NC_000913
35 Draws the map of the genome (version 3)
36 Created ggenomemap3.1.png
37
38 Go to the input files for this example
39 Go to the output files for this example
40
41 Command line arguments
42
43 Standard (Mandatory) qualifiers:
44 [-sequence] seqall Nucleotide sequence(s) filename and optional
45 format, or reference (input USA)
46
47 Additional (Optional) qualifiers: (none)
48 Advanced (Unprompted) qualifiers:
49 -format string [png] Output file format. Dependent on
50 'convert' command (Any string)
51 -width integer [8192] Image width (Any integer value)
52 -height integer [8192] Image height (Any integer value)
53 -[no]accid boolean [Y] Include to use sequence accession ID as
54 query
55 -goutfile string [ggenomemap3] Output file for non
56 interactive displays (Any string)
57
58 Associated qualifiers:
59
60 "-sequence" associated qualifiers
61 -sbegin1 integer Start of each sequence to be used
62 -send1 integer End of each sequence to be used
63 -sreverse1 boolean Reverse (if DNA)
64 -sask1 boolean Ask for begin/end/reverse
65 -snucleotide1 boolean Sequence is nucleotide
66 -sprotein1 boolean Sequence is protein
67 -slower1 boolean Make lower case
68 -supper1 boolean Make upper case
69 -scircular1 boolean Sequence is circular
70 -sformat1 string Input sequence format
71 -iquery1 string Input query fields or ID list
72 -ioffset1 integer Input start position offset
73 -sdbname1 string Database name
74 -sid1 string Entryname
75 -ufo1 string UFO features
76 -fformat1 string Features format
77 -fopenfile1 string Features file name
78
79 General qualifiers:
80 -auto boolean Turn off prompts
81 -stdout boolean Write first file to standard output
82 -filter boolean Read first file from standard input, write
83 first file to standard output
84 -options boolean Prompt for standard and additional values
85 -debug boolean Write debug output to program.dbg
86 -verbose boolean Report some/full command line options
87 -help boolean Report command line options and exit. More
88 information on associated and general
89 qualifiers can be found with -help -verbose
90 -warning boolean Report warnings
91 -error boolean Report errors
92 -fatal boolean Report fatal errors
93 -die boolean Report dying program messages
94 -version boolean Report version number and exit
95
96 Input file format
97
98 The database definitions for following commands are available at
99 http://soap.g-language.org/kbws/embossrc
100
101 ggenomemap3 reads one or more nucleotide sequences.
102
103 Output file format
104
105 The output from ggenomemap3 is to an image file.
106
107 Data files
108
109 None.
110
111 Notes
112
113 None.
114
115 References
116
117 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
118 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
119 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
120
121 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
122 large-scale analysis of high-throughput omics data, J. Pest Sci.,
123 31, 7.
124
125 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
126 Analysis Environment with REST and SOAP Web Service Interfaces,
127 Nucleic Acids Res., 38, W700-W705.
128
129 Warnings
130
131 None.
132
133 Diagnostic Error Messages
134
135 None.
136
137 Exit status
138
139 It always exits with a status of 0.
140
141 Known bugs
142
143 None.
144
145 See also
146
147 gcircularmap Draws circular map of the genome
148 gdnawalk Draws DNA Walk map of the genome
149
150 Author(s)
151
152 Hidetoshi Itaya (celery@g-language.org)
153 Institute for Advanced Biosciences, Keio University
154 252-0882 Japan
155
156 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
157 Institute for Advanced Biosciences, Keio University
158 252-0882 Japan
159
160 History
161
162 2012 - Written by Hidetoshi Itaya
163 2013 - Fixed by Hidetoshi Itaya
164
165 Target users
166
167 This program is intended to be used by everyone and everything, from
168 naive users to embedded scripts.
169
170 Comments
171
172 None.
173