|
0
|
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
|
