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

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1 goligomercounter
2 Function
3
4 Counts the number of given oligomers in a sequence
5
6 Description
7
8 goligomercounter counts the number of oligomers in a sequence (by windows
9 optionally). Oligomer can be specified using degenerate nucleotide alphabet,
10 or by regular expressions. k-mers can be counted by specifying the "-length"
11 qualifier.
12
13 G-language SOAP service is provided by the
14 Institute for Advanced Biosciences, Keio University.
15 The original web service is located at the following URL:
16
17 http://www.g-language.org/wiki/soap
18
19 WSDL(RPC/Encoded) file is located at:
20
21 http://soap.g-language.org/g-language.wsdl
22
23 Documentation on G-language Genome Analysis Environment methods are
24 provided at the Document Center
25
26 http://ws.g-language.org/gdoc/
27
28 Usage
29
30 Here is a sample session with goligomercounter
31
32 % goligomercounter refseqn:NC_000913 atgcatgc
33 Counts the number of given oligomers in a sequence
34 Program compseq output file [nc_000913.goligomercounter]:
35
36 Go to the input files for this example
37 Go to the output files for this example
38
39 Command line arguments
40
41 Standard (Mandatory) qualifiers:
42 [-sequence] seqall Nucleotide sequence(s) filename and optional
43 format, or reference (input USA)
44 [-oligomer] string Oligomer to count (Any string)
45 [-outfile] outfile [*.goligomercounter] Program compseq output
46 file
47
48 Additional (Optional) qualifiers: (none)
49 Advanced (Unprompted) qualifiers:
50 -window integer [0] Int window size (Any integer value)
51 -[no]accid boolean [Y] Include to use sequence accession ID as
52 query
53
54 Associated qualifiers:
55
56 "-sequence" associated qualifiers
57 -sbegin1 integer Start of each sequence to be used
58 -send1 integer End of each sequence to be used
59 -sreverse1 boolean Reverse (if DNA)
60 -sask1 boolean Ask for begin/end/reverse
61 -snucleotide1 boolean Sequence is nucleotide
62 -sprotein1 boolean Sequence is protein
63 -slower1 boolean Make lower case
64 -supper1 boolean Make upper case
65 -scircular1 boolean Sequence is circular
66 -sformat1 string Input sequence format
67 -iquery1 string Input query fields or ID list
68 -ioffset1 integer Input start position offset
69 -sdbname1 string Database name
70 -sid1 string Entryname
71 -ufo1 string UFO features
72 -fformat1 string Features format
73 -fopenfile1 string Features file name
74
75 "-outfile" associated qualifiers
76 -odirectory3 string Output directory
77
78 General qualifiers:
79 -auto boolean Turn off prompts
80 -stdout boolean Write first file to standard output
81 -filter boolean Read first file from standard input, write
82 first file to standard output
83 -options boolean Prompt for standard and additional values
84 -debug boolean Write debug output to program.dbg
85 -verbose boolean Report some/full command line options
86 -help boolean Report command line options and exit. More
87 information on associated and general
88 qualifiers can be found with -help -verbose
89 -warning boolean Report warnings
90 -error boolean Report errors
91 -fatal boolean Report fatal errors
92 -die boolean Report dying program messages
93 -version boolean Report version number and exit
94
95 Input file format
96
97 The database definitions for following commands are available at
98 http://soap.g-language.org/kbws/embossrc
99
100 goligomercounter reads one or more nucleotide sequences.
101
102 Output file format
103
104 The output from goligomercounter is to a plain text file.
105
106 File: nc_000913.goligomercounter
107
108 Sequence: NC_000913 Oligomer: atgcatgc Number: 27
109
110
111 Data files
112
113 None.
114
115 Notes
116
117 None.
118
119 References
120
121 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
122 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
123 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
124
125 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
126 large-scale analysis of high-throughput omics data, J. Pest Sci.,
127 31, 7.
128
129 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
130 Analysis Environment with REST and SOAP Web Service Interfaces,
131 Nucleic Acids Res., 38, W700-W705.
132
133 Warnings
134
135 None.
136
137 Diagnostic Error Messages
138
139 None.
140
141 Exit status
142
143 It always exits with a status of 0.
144
145 Known bugs
146
147 None.
148
149 See also
150
151 gkmertable Create an image showing all k-mer abundance within a
152 sequence
153 gnucleotideperiodicity Checks the periodicity of certain oligonucleotides
154 goligomersearch Searches oligomers in given sequence
155 gsignature Calculate oligonucleotide usage (genomic signature)
156
157 Author(s)
158
159 Hidetoshi Itaya (celery@g-language.org)
160 Institute for Advanced Biosciences, Keio University
161 252-0882 Japan
162
163 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
164 Institute for Advanced Biosciences, Keio University
165 252-0882 Japan
166
167 History
168
169 2012 - Written by Hidetoshi Itaya
170 2013 - Fixed by Hidetoshi Itaya
171
172 Target users
173
174 This program is intended to be used by everyone and everything, from
175 naive users to embedded scripts.
176
177 Comments
178
179 None.
180