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1 gentrez
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2 Function
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3
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4 Search NCBI Entrez
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5
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6 Description
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7
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8 gentrez searches NCBI Entrez with keyword through EUtilities.
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9 This is intended for quick lookup through the command line
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10 so only top ten hits are reported.
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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 gentrez
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30
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31 % gentrez genome 'Escherichia coli'
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32 Search NCBI Entrez
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33 ASCII text output file [genome.Escherichia coli.gentrez]:
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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 [-database] string [pubmed] NCBI database to search (Any
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42 string)
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43 [-query] string Query to search (Any string)
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44 [-outfile] outfile [$(database).$(query).gentrez] ASCII text
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45 output file
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46
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47 Additional (Optional) qualifiers: (none)
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48 Advanced (Unprompted) qualifiers: (none)
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49 Associated qualifiers:
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50
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51 "-outfile" associated qualifiers
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52 -odirectory3 string Output directory
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53
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54 General qualifiers:
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55 -auto boolean Turn off prompts
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56 -stdout boolean Write first file to standard output
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57 -filter boolean Read first file from standard input, write
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58 first file to standard output
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59 -options boolean Prompt for standard and additional values
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60 -debug boolean Write debug output to program.dbg
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61 -verbose boolean Report some/full command line options
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62 -help boolean Report command line options and exit. More
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63 information on associated and general
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64 qualifiers can be found with -help -verbose
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65 -warning boolean Report warnings
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66 -error boolean Report errors
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67 -fatal boolean Report fatal errors
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68 -die boolean Report dying program messages
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69 -version boolean Report version number and exit
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70
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71 Input file format
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72
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73 The database definitions for following commands are available at
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74 http://soap.g-language.org/kbws/embossrc
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75
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76 gentrez reads no file input.
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77
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78 Output file format
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79
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80 The output from gentrez is to a plain text file.
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81
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82 File: genome.Escherichia coli.gentrez
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83
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84 53 entries found in NUCLEOTIDE: (Showing up to 10 hits)
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85
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86 1. Accession Number: NZ_AKBV01000001
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87 Escherichia coli str. K-12 substr. MG1655 strain K-12 cont1.1 chromosome, whole genome shotgun sequence, complete genome
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88
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89 2. Accession Number: NC_018658
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90 Escherichia coli O104:H4 str. 2011C-3493 chromosome, complete genome
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91
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92 3. Accession Number: NC_012971
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93 Escherichia coli BL21(DE3) chromosome, complete genome
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94
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95 4. Accession Number: NC_017635
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96 Escherichia coli W chromosome, complete genome
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97
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98 5. Accession Number: NC_018650
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99 Escherichia coli O104:H4 str. 2009EL-2050 chromosome, complete genome
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100
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101 6. Accession Number: NC_018661
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102 Escherichia coli O104:H4 str. 2009EL-2071 chromosome, complete genome
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103
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104 7. Accession Number: NC_017906
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105 Escherichia coli Xuzhou21 chromosome, complete genome
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106
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107 8. Accession Number: NC_017634
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108 Escherichia coli O83:H1 str. NRG 857C chromosome, complete genome
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109
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110 9. Accession Number: NC_017656
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111 Escherichia coli O55:H7 str. RM12579 chromosome, complete genome
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112
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113 10. Accession Number: NC_017664
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114 Escherichia coli W chromosome, complete genome
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115
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116
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117 Data files
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118
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119 None.
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120
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121 Notes
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122
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123 None.
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124
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125 References
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126
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127 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
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128 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
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129 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
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130
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131 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
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132 large-scale analysis of high-throughput omics data, J. Pest Sci.,
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133 31, 7.
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134
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135 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
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136 Analysis Environment with REST and SOAP Web Service Interfaces,
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137 Nucleic Acids Res., 38, W700-W705.
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138
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139 Warnings
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140
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141 None.
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142
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143 Diagnostic Error Messages
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144
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145 None.
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146
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147 Exit status
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148
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149 It always exits with a status of 0.
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150
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151 Known bugs
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152
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153 None.
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154
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155 See also
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156
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157 None.
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158
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159 Author(s)
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160
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161 Hidetoshi Itaya (celery@g-language.org)
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162 Institute for Advanced Biosciences, Keio University
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163 252-0882 Japan
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164
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165 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
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166 Institute for Advanced Biosciences, Keio University
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167 252-0882 Japan
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168
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169 History
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170
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171 2012 - Written by Hidetoshi Itaya
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172 2013 - Fixed by Hidetoshi Itaya
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173
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174 Target users
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175
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176 This program is intended to be used by everyone and everything, from
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177 naive users to embedded scripts.
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178
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179 Comments
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180
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181 None.
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182
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