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comparison GEMBASSY-1.0.3/doc/text/gseq2png.txt @ 2:8947fca5f715 draft default tip

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date Fri, 26 Jun 2015 05:21:44 -0400
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1 gseq2png
2 Function
3
4 Converts a sequence to PNG image
5
6 Description
7
8 gseq2png converts a sequence to a png image, by representing nucleotide
9 sequences with representative pixels. A is shown in red, T is shown in
10 green, G is shown in yellow, and C is shown in blue.
11
12 G-language SOAP service is provided by the
13 Institute for Advanced Biosciences, Keio University.
14 The original web service is located at the following URL:
15
16 http://www.g-language.org/wiki/soap
17
18 WSDL(RPC/Encoded) file is located at:
19
20 http://soap.g-language.org/g-language.wsdl
21
22 Documentation on G-language Genome Analysis Environment methods are
23 provided at the Document Center
24
25 http://ws.g-language.org/gdoc/
26
27 Usage
28
29 Here is a sample session with gseq2png
30
31 % gseq2png refseqn:NC_000913
32 Converts a sequence to PNG image
33 Created gseq2png.1.png
34
35 Go to the input files for this example
36 Go to the output files for this example
37
38 Command line arguments
39
40 Standard (Mandatory) qualifiers:
41 [-sequence] seqall Nucleotide sequence(s) filename and optional
42 format, or reference (input USA)
43
44 Additional (Optional) qualifiers: (none)
45 Advanced (Unprompted) qualifiers:
46 -format string [png] Output file format. Dependent on
47 'convert' command (Any string)
48 -width integer [640] Width of the image (Any integer value)
49 -window integer [20] Window size of a sequence to represent
50 each pixel (Any integer value)
51 -goutfile string [gcgr] Output file for non interactive
52 displays (Any string)
53
54 Associated qualifiers:
55
56 "-sequence" associated qualifiers
57 -sbegin1 integer Start of each sequence to be used
58 -send1 integer End of each sequence to be used
59 -sreverse1 boolean Reverse (if DNA)
60 -sask1 boolean Ask for begin/end/reverse
61 -snucleotide1 boolean Sequence is nucleotide
62 -sprotein1 boolean Sequence is protein
63 -slower1 boolean Make lower case
64 -supper1 boolean Make upper case
65 -scircular1 boolean Sequence is circular
66 -sformat1 string Input sequence format
67 -iquery1 string Input query fields or ID list
68 -ioffset1 integer Input start position offset
69 -sdbname1 string Database name
70 -sid1 string Entryname
71 -ufo1 string UFO features
72 -fformat1 string Features format
73 -fopenfile1 string Features file name
74
75 General qualifiers:
76 -auto boolean Turn off prompts
77 -stdout boolean Write first file to standard output
78 -filter boolean Read first file from standard input, write
79 first file to standard output
80 -options boolean Prompt for standard and additional values
81 -debug boolean Write debug output to program.dbg
82 -verbose boolean Report some/full command line options
83 -help boolean Report command line options and exit. More
84 information on associated and general
85 qualifiers can be found with -help -verbose
86 -warning boolean Report warnings
87 -error boolean Report errors
88 -fatal boolean Report fatal errors
89 -die boolean Report dying program messages
90 -version boolean Report version number and exit
91
92 Input file format
93
94 The database definitions for following commands are available at
95 http://soap.g-language.org/kbws/embossrc
96
97 gseq2png reads one or more nucleotide sequences.
98
99 Output file format
100
101 The output from gseq2png is to an image file.
102
103
104
105 Data files
106
107 None.
108
109 Notes
110
111 None.
112
113 References
114
115 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
116 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
117 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
118
119 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
120 large-scale analysis of high-throughput omics data, J. Pest Sci.,
121 31, 7.
122
123 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
124 Analysis Environment with REST and SOAP Web Service Interfaces,
125 Nucleic Acids Res., 38, W700-W705.
126
127 Warnings
128
129 None.
130
131 Diagnostic Error Messages
132
133 None.
134
135 Exit status
136
137 It always exits with a status of 0.
138
139 Known bugs
140
141 None.
142
143 See also
144
145 gcgr Create a Chaos Game Representation of a given sequence
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