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1 gseq2png
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2 Function
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3
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4 Converts a sequence to PNG image
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5
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6 Description
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7
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8 gseq2png converts a sequence to a png image, by representing nucleotide
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9 sequences with representative pixels. A is shown in red, T is shown in
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10 green, G is shown in yellow, and C is shown in blue.
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11
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12 G-language SOAP service is provided by the
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13 Institute for Advanced Biosciences, Keio University.
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14 The original web service is located at the following URL:
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15
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16 http://www.g-language.org/wiki/soap
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17
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18 WSDL(RPC/Encoded) file is located at:
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19
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20 http://soap.g-language.org/g-language.wsdl
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21
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22 Documentation on G-language Genome Analysis Environment methods are
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23 provided at the Document Center
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24
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25 http://ws.g-language.org/gdoc/
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26
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27 Usage
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28
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29 Here is a sample session with gseq2png
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30
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31 % gseq2png refseqn:NC_000913
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32 Converts a sequence to PNG image
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33 Created gseq2png.1.png
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34
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35 Go to the input files for this example
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36 Go to the output files for this example
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37
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38 Command line arguments
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39
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40 Standard (Mandatory) qualifiers:
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41 [-sequence] seqall Nucleotide sequence(s) filename and optional
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42 format, or reference (input USA)
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43
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44 Additional (Optional) qualifiers: (none)
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45 Advanced (Unprompted) qualifiers:
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46 -format string [png] Output file format. Dependent on
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47 'convert' command (Any string)
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48 -width integer [640] Width of the image (Any integer value)
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49 -window integer [20] Window size of a sequence to represent
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50 each pixel (Any integer value)
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51 -goutfile string [gcgr] Output file for non interactive
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52 displays (Any string)
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53
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54 Associated qualifiers:
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55
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56 "-sequence" associated qualifiers
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57 -sbegin1 integer Start of each sequence to be used
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58 -send1 integer End of each sequence to be used
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59 -sreverse1 boolean Reverse (if DNA)
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60 -sask1 boolean Ask for begin/end/reverse
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61 -snucleotide1 boolean Sequence is nucleotide
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62 -sprotein1 boolean Sequence is protein
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63 -slower1 boolean Make lower case
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64 -supper1 boolean Make upper case
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65 -scircular1 boolean Sequence is circular
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66 -sformat1 string Input sequence format
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67 -iquery1 string Input query fields or ID list
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68 -ioffset1 integer Input start position offset
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69 -sdbname1 string Database name
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70 -sid1 string Entryname
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71 -ufo1 string UFO features
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72 -fformat1 string Features format
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73 -fopenfile1 string Features file name
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74
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75 General qualifiers:
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76 -auto boolean Turn off prompts
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77 -stdout boolean Write first file to standard output
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78 -filter boolean Read first file from standard input, write
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79 first file to standard output
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80 -options boolean Prompt for standard and additional values
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81 -debug boolean Write debug output to program.dbg
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82 -verbose boolean Report some/full command line options
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83 -help boolean Report command line options and exit. More
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84 information on associated and general
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85 qualifiers can be found with -help -verbose
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86 -warning boolean Report warnings
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87 -error boolean Report errors
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88 -fatal boolean Report fatal errors
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89 -die boolean Report dying program messages
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90 -version boolean Report version number and exit
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91
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92 Input file format
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93
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94 The database definitions for following commands are available at
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95 http://soap.g-language.org/kbws/embossrc
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96
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97 gseq2png reads one or more nucleotide sequences.
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98
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99 Output file format
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100
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101 The output from gseq2png is to an image file.
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102
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103
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104
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105 Data files
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106
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107 None.
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108
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109 Notes
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110
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111 None.
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112
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113 References
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114
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115 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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116 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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117 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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118
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119 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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120 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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121 31, 7.
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122
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123 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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124 Analysis Environment with REST and SOAP Web Service Interfaces,
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125 Nucleic Acids Res., 38, W700-W705.
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126
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127 Warnings
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128
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129 None.
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130
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131 Diagnostic Error Messages
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132
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133 None.
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134
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135 Exit status
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136
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137 It always exits with a status of 0.
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138
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139 Known bugs
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140
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141 None.
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142
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143 See also
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144
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145 gcgr Create a Chaos Game Representation of a given sequence
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146
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147 Author(s)
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148
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149 Hidetoshi Itaya (celery@g-language.org)
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150 Institute for Advanced Biosciences, Keio University
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151 252-0882 Japan
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152
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153 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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154 Institute for Advanced Biosciences, Keio University
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155 252-0882 Japan
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156
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157 History
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158
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159 2012 - Written by Hidetoshi Itaya
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160 2013 - Fixed by Hidetoshi Itaya
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161
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162 Target users
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163
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164 This program is intended to be used by everyone and everything, from
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165 naive users to embedded scripts.
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166
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167 Comments
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168
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169 None.
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170
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