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

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1 gseqinfo
2 Function
3
4 Prints out basic nucleotide sequence statistics
5
6 Description
7
8 gseqinfo prints out basic nucleotide sequence statistics of the given
9 nucleotide sequence. It returns the number of A, T, G, and C bases.
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 gseqinfo
29
30 % gseqinfo refseqn:NC_000913
31 Prints out basic nucleotide sequence statistics
32 Program compseq output file [nc_000913.gseqinfo]:
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 [-outfile] outfile [*.gseqinfo] Program compseq output file
43
44 Additional (Optional) qualifiers: (none)
45 Advanced (Unprompted) qualifiers: (none)
46 Associated qualifiers:
47
48 "-sequence" associated qualifiers
49 -sbegin1 integer Start of each sequence to be used
50 -send1 integer End of each sequence to be used
51 -sreverse1 boolean Reverse (if DNA)
52 -sask1 boolean Ask for begin/end/reverse
53 -snucleotide1 boolean Sequence is nucleotide
54 -sprotein1 boolean Sequence is protein
55 -slower1 boolean Make lower case
56 -supper1 boolean Make upper case
57 -scircular1 boolean Sequence is circular
58 -sformat1 string Input sequence format
59 -iquery1 string Input query fields or ID list
60 -ioffset1 integer Input start position offset
61 -sdbname1 string Database name
62 -sid1 string Entryname
63 -ufo1 string UFO features
64 -fformat1 string Features format
65 -fopenfile1 string Features file name
66
67 "-outfile" associated qualifiers
68 -odirectory2 string Output directory
69
70 General qualifiers:
71 -auto boolean Turn off prompts
72 -stdout boolean Write first file to standard output
73 -filter boolean Read first file from standard input, write
74 first file to standard output
75 -options boolean Prompt for standard and additional values
76 -debug boolean Write debug output to program.dbg
77 -verbose boolean Report some/full command line options
78 -help boolean Report command line options and exit. More
79 information on associated and general
80 qualifiers can be found with -help -verbose
81 -warning boolean Report warnings
82 -error boolean Report errors
83 -fatal boolean Report fatal errors
84 -die boolean Report dying program messages
85 -version boolean Report version number and exit
86
87 Input file format
88
89 The database definitions for following commands are available at
90 http://soap.g-language.org/kbws/embossrc
91
92 gseqinfo reads one or more nucleotide sequences.
93
94 Output file format
95
96 The output from gseqinfo is to a plain text file.
97
98 File: nc_000913.gseqinfo
99
100 Sequence: NC_000913 A: 1142228 T: 1140970 G: 1176923 C: 1179555
101
102
103 Data files
104
105 None.
106
107 Notes
108
109 None.
110
111 References
112
113 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
114 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
115 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
116
117 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
118 large-scale analysis of high-throughput omics data, J. Pest Sci.,
119 31, 7.
120
121 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
122 Analysis Environment with REST and SOAP Web Service Interfaces,
123 Nucleic Acids Res., 38, W700-W705.
124
125 Warnings
126
127 None.
128
129 Diagnostic Error Messages
130
131 None.
132
133 Exit status
134
135 It always exits with a status of 0.
136
137 Known bugs
138
139 None.
140
141 See also
142
143 gconsensus_z Calculate consensus in given array of sequences
144 gdist_in_cc Calculates the distance between two loci in circular chromosomes
145 gpalindrome Searches palindrome sequences
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