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1 gqueryarm
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2 Function
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3
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4 Get the replication arm name (left or right) from the given position
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5
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6 Description
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7
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8 gqueryarm returns whether the given position is in the left or right arm of
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9 a circular chromosome.
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10
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11 G-language SOAP service is provided by the
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12 Institute for Advanced Biosciences, Keio University.
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13 The original web service is located at the following URL:
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14
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15 http://www.g-language.org/wiki/soap
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16
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17 WSDL(RPC/Encoded) file is located at:
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18
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19 http://soap.g-language.org/g-language.wsdl
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20
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21 Documentation on G-language Genome Analysis Environment methods are
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22 provided at the Document Center
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23
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24 http://ws.g-language.org/gdoc/
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25
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26 Usage
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27
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28 Here is a sample session with gqueryarm
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29
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30 % gqueryarm refseqn:NC_000913 1234
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31 Get the replication arm name (left or right) from the given position
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32 Output file [nc_000913.gqueryarm]:
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33
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34 Go to the input files for this example
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35 Go to the output files for this example
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36
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37 Command line arguments
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38
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39 Standard (Mandatory) qualifiers:
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40 [-sequence] seqall Nucleotide sequence(s) filename and optional
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41 format, or reference (input USA)
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42 [-position] integer [0] Position to query (Any integer value)
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43 [-outfile] outfile [*.gqueryarm] Output file name
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44
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45 Additional (Optional) qualifiers: (none)
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46 Advanced (Unprompted) qualifiers:
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47 -[no]accid boolean [Y] Include to use sequence accession ID as
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48 query
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49
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50 Associated qualifiers:
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51
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52 "-sequence" associated qualifiers
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53 -sbegin1 integer Start of each sequence to be used
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54 -send1 integer End of each sequence to be used
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55 -sreverse1 boolean Reverse (if DNA)
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56 -sask1 boolean Ask for begin/end/reverse
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57 -snucleotide1 boolean Sequence is nucleotide
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58 -sprotein1 boolean Sequence is protein
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59 -slower1 boolean Make lower case
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60 -supper1 boolean Make upper case
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61 -scircular1 boolean Sequence is circular
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62 -sformat1 string Input sequence format
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63 -iquery1 string Input query fields or ID list
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64 -ioffset1 integer Input start position offset
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65 -sdbname1 string Database name
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66 -sid1 string Entryname
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67 -ufo1 string UFO features
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68 -fformat1 string Features format
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69 -fopenfile1 string Features file name
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70
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71 "-outfile" associated qualifiers
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72 -odirectory3 string Output directory
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73
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74 General qualifiers:
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75 -auto boolean Turn off prompts
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76 -stdout boolean Write first file to standard output
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77 -filter boolean Read first file from standard input, write
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78 first file to standard output
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79 -options boolean Prompt for standard and additional values
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80 -debug boolean Write debug output to program.dbg
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81 -verbose boolean Report some/full command line options
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82 -help boolean Report command line options and exit. More
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83 information on associated and general
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84 qualifiers can be found with -help -verbose
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85 -warning boolean Report warnings
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86 -error boolean Report errors
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87 -fatal boolean Report fatal errors
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88 -die boolean Report dying program messages
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89 -version boolean Report version number and exit
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90
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91 Input file format
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92
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93 The database definitions for following commands are available at
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94 http://soap.g-language.org/kbws/embossrc
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95
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96 gqueryarm reads one or more nucleotide sequences.
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97
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98 Output file format
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99
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100 The output from gqueryarm is to a plain text file.
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101
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102 File: nc_000913.gqueryarm
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103
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104 Sequence: NC_000913 Arm: right
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105
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106
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107 Data files
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108
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109 None.
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110
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111 Notes
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112
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113 None.
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114
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115 References
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116
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117 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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118 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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119 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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120
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121 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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122 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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123 31, 7.
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124
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125 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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126 Analysis Environment with REST and SOAP Web Service Interfaces,
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127 Nucleic Acids Res., 38, W700-W705.
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128
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129 Warnings
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130
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131 None.
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132
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133 Diagnostic Error Messages
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134
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135 None.
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136
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137 Exit status
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138
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139 It always exits with a status of 0.
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140
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141 Known bugs
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142
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143 None.
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144
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145 See also
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146
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147 gquery_strand Get the strand name (leading or lagging) from the given
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148 position
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149
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150 Author(s)
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151
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152 Hidetoshi Itaya (celery@g-language.org)
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153 Institute for Advanced Biosciences, Keio University
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154 252-0882 Japan
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155
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156 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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157 Institute for Advanced Biosciences, Keio University
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158 252-0882 Japan
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159
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160 History
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161
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162 2012 - Written by Hidetoshi Itaya
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163 2013 - Fixed by Hidetoshi Itaya
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164
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165 Target users
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166
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167 This program is intended to be used by everyone and everything, from
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168 naive users to embedded scripts.
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169
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170 Comments
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171
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172 None.
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173
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