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

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1 gqueryarm
2 Function
3
4 Get the replication arm name (left or right) from the given position
5
6 Description
7
8 gqueryarm returns whether the given position is in the left or right arm of
9 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 gqueryarm
29
30 % gqueryarm refseqn:NC_000913 1234
31 Get the replication arm name (left or right) from the given position
32 Output file [nc_000913.gqueryarm]:
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 [*.gqueryarm] Output file name
44
45 Additional (Optional) qualifiers: (none)
46 Advanced (Unprompted) qualifiers:
47 -[no]accid boolean [Y] Include to use sequence accession ID as
48 query
49
50 Associated qualifiers:
51
52 "-sequence" associated qualifiers
53 -sbegin1 integer Start of each sequence to be used
54 -send1 integer End of each sequence to be used
55 -sreverse1 boolean Reverse (if DNA)
56 -sask1 boolean Ask for begin/end/reverse
57 -snucleotide1 boolean Sequence is nucleotide
58 -sprotein1 boolean Sequence is protein
59 -slower1 boolean Make lower case
60 -supper1 boolean Make upper case
61 -scircular1 boolean Sequence is circular
62 -sformat1 string Input sequence format
63 -iquery1 string Input query fields or ID list
64 -ioffset1 integer Input start position offset
65 -sdbname1 string Database name
66 -sid1 string Entryname
67 -ufo1 string UFO features
68 -fformat1 string Features format
69 -fopenfile1 string Features file name
70
71 "-outfile" associated qualifiers
72 -odirectory3 string Output directory
73
74 General qualifiers:
75 -auto boolean Turn off prompts
76 -stdout boolean Write first file to standard output
77 -filter boolean Read first file from standard input, write
78 first file to standard output
79 -options boolean Prompt for standard and additional values
80 -debug boolean Write debug output to program.dbg
81 -verbose boolean Report some/full command line options
82 -help boolean Report command line options and exit. More
83 information on associated and general
84 qualifiers can be found with -help -verbose
85 -warning boolean Report warnings
86 -error boolean Report errors
87 -fatal boolean Report fatal errors
88 -die boolean Report dying program messages
89 -version boolean Report version number and exit
90
91 Input file format
92
93 The database definitions for following commands are available at
94 http://soap.g-language.org/kbws/embossrc
95
96 gqueryarm reads one or more nucleotide sequences.
97
98 Output file format
99
100 The output from gqueryarm is to a plain text file.
101
102 File: nc_000913.gqueryarm
103
104 Sequence: NC_000913 Arm: right
105
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 gquery_strand Get the strand name (leading or lagging) from the given
148 position
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