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

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1 ggcwin
2 Function
3
4 Calculates the GC content along the given genome
5
6 Description
7
8 ggcwin calculates and plots the GC content of the given sequence.
9
10 G-language SOAP service is provided by the
11 Institute for Advanced Biosciences, Keio University.
12 The original web service is located at the following URL:
13
14 http://www.g-language.org/wiki/soap
15
16 WSDL(RPC/Encoded) file is located at:
17
18 http://soap.g-language.org/g-language.wsdl
19
20 Documentation on G-language Genome Analysis Environment methods are
21 provided at the Document Center
22
23 http://ws.g-language.org/gdoc/
24
25 Usage
26
27 Here is a sample session with ggcwin
28
29 % ggcwin refseqn:NC_000913
30 Calculates the GC content along the given genome
31 Program compseq output file (optional) [nc_000913.ggcwin]:
32
33 Go to the input files for this example
34 Go to the output files for this example
35
36 Example 2
37
38 % ggcwin refseqn:NC_000913 -plot -graph png
39 Calculates the GC content along the given genome
40 Created ggcwin.1.png
41
42 Go to the input files for this example
43 Go to the output files for this example
44
45 Command line arguments
46
47 Standard (Mandatory) qualifiers (* if not always prompted):
48 [-sequence] seqall Nucleotide sequence(s) filename and optional
49 format, or reference (input USA)
50 * -graph xygraph [$EMBOSS_GRAPHICS value, or x11] Graph type
51 (ps, hpgl, hp7470, hp7580, meta, cps, x11,
52 tek, tekt, none, data, xterm, png, gif, svg)
53 * -outfile outfile [*.ggcwin] Program compseq output file
54 (optional)
55
56 Additional (Optional) qualifiers: (none)
57 Advanced (Unprompted) qualifiers:
58 -window integer [10000] Window size to observe (Any integer
59 value)
60 -at boolean [N] Include for observing AT skew instead of
61 GC skew
62 -purine boolean [N] Include for observing purine (AG/TC)
63 skew
64 -keto boolean [N] Include for observing keto (TG/AC) skew
65 default: "0
66 -plot toggle [N] Include to plot result
67
68 Associated qualifiers:
69
70 "-sequence" associated qualifiers
71 -sbegin1 integer Start of each sequence to be used
72 -send1 integer End of each sequence to be used
73 -sreverse1 boolean Reverse (if DNA)
74 -sask1 boolean Ask for begin/end/reverse
75 -snucleotide1 boolean Sequence is nucleotide
76 -sprotein1 boolean Sequence is protein
77 -slower1 boolean Make lower case
78 -supper1 boolean Make upper case
79 -scircular1 boolean Sequence is circular
80 -sformat1 string Input sequence format
81 -iquery1 string Input query fields or ID list
82 -ioffset1 integer Input start position offset
83 -sdbname1 string Database name
84 -sid1 string Entryname
85 -ufo1 string UFO features
86 -fformat1 string Features format
87 -fopenfile1 string Features file name
88
89 "-graph" associated qualifiers
90 -gprompt boolean Graph prompting
91 -gdesc string Graph description
92 -gtitle string Graph title
93 -gsubtitle string Graph subtitle
94 -gxtitle string Graph x axis title
95 -gytitle string Graph y axis title
96 -goutfile string Output file for non interactive displays
97 -gdirectory string Output directory
98
99 "-outfile" associated qualifiers
100 -odirectory string Output directory
101
102 General qualifiers:
103 -auto boolean Turn off prompts
104 -stdout boolean Write first file to standard output
105 -filter boolean Read first file from standard input, write
106 first file to standard output
107 -options boolean Prompt for standard and additional values
108 -debug boolean Write debug output to program.dbg
109 -verbose boolean Report some/full command line options
110 -help boolean Report command line options and exit. More
111 information on associated and general
112 qualifiers can be found with -help -verbose
113 -warning boolean Report warnings
114 -error boolean Report errors
115 -fatal boolean Report fatal errors
116 -die boolean Report dying program messages
117 -version boolean Report version number and exit
118
119 Input file format
120
121 The database definitions for following commands are available at
122 http://soap.g-language.org/kbws/embossrc
123
124 ggcwin reads one or more nucleotide sequences.
125
126 Output file format
127
128 The output from ggcwin is to a plain text file or the EMBOSS graphics device.
129
130 File: nc_000913.ggcwin
131
132 Sequence: NC_000913
133 location,GC content
134 0,0.520700
135 10000,0.499400
136 20000,0.526200
137 30000,0.532300
138 40000,0.527700
139 50000,0.515600
140 60000,0.555800
141 70000,0.536000
142
143 [Part of this file has been deleted for brevity]
144
145 4530000,0.442800
146 4540000,0.487000
147 4550000,0.507700
148 4560000,0.509600
149 4570000,0.444600
150 4580000,0.531600
151 4590000,0.512300
152 4600000,0.504500
153 4610000,0.535600
154 4620000,0.546600
155
156
157 Data files
158
159 None.
160
161 Notes
162
163 None.
164
165 References
166
167 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
168 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
169 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
170
171 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
172 large-scale analysis of high-throughput omics data, J. Pest Sci.,
173 31, 7.
174
175 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
176 Analysis Environment with REST and SOAP Web Service Interfaces,
177 Nucleic Acids Res., 38, W700-W705.
178
179 Warnings
180
181 None.
182
183 Diagnostic Error Messages
184
185 None.
186
187 Exit status
188
189 It always exits with a status of 0.
190
191 Known bugs
192
193 None.
194
195 See also
196
197 ggcskew Calculates the GC skew of the input sequence
198 ggeneskew Calculate the gene strand bias of the given genome
199 ggenomicskew Calculates the GC skew in different regions of the given genom
200
201 Author(s)
202
203 Hidetoshi Itaya (celery@g-language.org)
204 Institute for Advanced Biosciences, Keio University
205 252-0882 Japan
206
207 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
208 Institute for Advanced Biosciences, Keio University
209 252-0882 Japan
210
211 History
212
213 2012 - Written by Hidetoshi Itaya
214 2013 - Fixed by Hidetoshi Itaya
215
216 Target users
217
218 This program is intended to be used by everyone and everything, from
219 naive users to embedded scripts.
220
221 Comments
222
223 None.
224