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

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1 gquerystrand
2 Function
3
4 Get the strand name (leading or lagging) from the given position
5
6 Description
7
8 gquerystrand returns whether the given position is in the leading or lagging
9 strand of a circular chromosome.
10
11 G-language SOAP service is provided by the
12 Institute for Advanced Biosciences, Keio University.
13 The original web service is located at the following URL:
14
15 http://www.g-language.org/wiki/soap
16
17 WSDL(RPC/Encoded) file is located at:
18
19 http://soap.g-language.org/g-language.wsdl
20
21 Documentation on G-language Genome Analysis Environment methods are
22 provided at the Document Center
23
24 http://ws.g-language.org/gdoc/
25
26 Usage
27
28 Here is a sample session with gquerystrand
29
30 % gquerystrand refseqn:NC_000913 1234
31 Get the strand name (leading or lagging) from the given position
32 Output file [nc_000913.gquerystrand]:
33
34 Go to the input files for this example
35 Go to the output files for this example
36
37 Command line arguments
38
39 Standard (Mandatory) qualifiers:
40 [-sequence] seqall Nucleotide sequence(s) filename and optional
41 format, or reference (input USA)
42 [-position] integer [0] Position to query (Any integer value)
43 [-outfile] outfile [*.gquerystrand] Output file name
44
45 Additional (Optional) qualifiers: (none)
46 Advanced (Unprompted) qualifiers:
47 -direction selection [direct] Strand of the querying position
48 either 'direct' or 'complement'
49 -[no]accid boolean [Y] Include to use sequence accession ID as
50 query
51
52 Associated qualifiers:
53
54 "-sequence" associated qualifiers
55 -sbegin1 integer Start of each sequence to be used
56 -send1 integer End of each sequence to be used
57 -sreverse1 boolean Reverse (if DNA)
58 -sask1 boolean Ask for begin/end/reverse
59 -snucleotide1 boolean Sequence is nucleotide
60 -sprotein1 boolean Sequence is protein
61 -slower1 boolean Make lower case
62 -supper1 boolean Make upper case
63 -scircular1 boolean Sequence is circular
64 -sformat1 string Input sequence format
65 -iquery1 string Input query fields or ID list
66 -ioffset1 integer Input start position offset
67 -sdbname1 string Database name
68 -sid1 string Entryname
69 -ufo1 string UFO features
70 -fformat1 string Features format
71 -fopenfile1 string Features file name
72
73 "-outfile" associated qualifiers
74 -odirectory3 string Output directory
75
76 General qualifiers:
77 -auto boolean Turn off prompts
78 -stdout boolean Write first file to standard output
79 -filter boolean Read first file from standard input, write
80 first file to standard output
81 -options boolean Prompt for standard and additional values
82 -debug boolean Write debug output to program.dbg
83 -verbose boolean Report some/full command line options
84 -help boolean Report command line options and exit. More
85 information on associated and general
86 qualifiers can be found with -help -verbose
87 -warning boolean Report warnings
88 -error boolean Report errors
89 -fatal boolean Report fatal errors
90 -die boolean Report dying program messages
91 -version boolean Report version number and exit
92
93 Input file format
94
95 The database definitions for following commands are available at
96 http://soap.g-language.org/kbws/embossrc
97
98 gquerystrand reads one or more nucleotide sequences.
99
100 Output file format
101
102 The output from gquerystrand is to a plain text file.
103
104 File: nc_000913.gquerystrand
105
106 Sequence: NC_000913 Strand: leading
107
108
109 Data files
110
111 None.
112
113 Notes
114
115 None.
116
117 References
118
119 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
120 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
121 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
122
123 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
124 large-scale analysis of high-throughput omics data, J. Pest Sci.,
125 31, 7.
126
127 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
128 Analysis Environment with REST and SOAP Web Service Interfaces,
129 Nucleic Acids Res., 38, W700-W705.
130
131 Warnings
132
133 None.
134
135 Diagnostic Error Messages
136
137 None.
138
139 Exit status
140
141 It always exits with a status of 0.
142
143 Known bugs
144
145 None.
146
147 See also
148
149 gquery_arm Get the replication arm name (left or right) from the given
150 position
151
152 Author(s)
153
154 Hidetoshi Itaya (celery@g-language.org)
155 Institute for Advanced Biosciences, Keio University
156 252-0882 Japan
157
158 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
159 Institute for Advanced Biosciences, Keio University
160 252-0882 Japan
161
162 History
163
164 2012 - Written by Hidetoshi Itaya
165 2013 - Fixed by Hidetoshi Itaya
166
167 Target users
168
169 This program is intended to be used by everyone and everything, from
170 naive users to embedded scripts.
171
172 Comments
173
174 None.
175