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comparison GEMBASSY-1.0.3/doc/text/ggenomemap3.txt @ 2:8947fca5f715 draft default tip
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author | ktnyt |
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date | Fri, 26 Jun 2015 05:21:44 -0400 |
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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 |