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annotate libs/sratoolkit.2.8.0-centos_linux64/schema/sra/generic-fastq.vschema @ 3:38ad1130d077 draft

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author charles_s_test
date Mon, 27 Nov 2017 11:21:07 -0500
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1 /*===========================================================================
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2 *
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3 * PUBLIC DOMAIN NOTICE
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4 * National Center for Biotechnology Information
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5 *
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6 * This software/database is a "United States Government Work" under the
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7 * terms of the United States Copyright Act. It was written as part of
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8 * the author's official duties as a United States Government employee and
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9 * thus cannot be copyrighted. This software/database is freely available
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10 * to the public for use. The National Library of Medicine and the U.S.
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11 * Government have not placed any restriction on its use or reproduction.
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12 *
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13 * Although all reasonable efforts have been taken to ensure the accuracy
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14 * and reliability of the software and data, the NLM and the U.S.
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15 * Government do not and cannot warrant the performance or results that
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16 * may be obtained by using this software or data. The NLM and the U.S.
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17 * Government disclaim all warranties, express or implied, including
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18 * warranties of performance, merchantability or fitness for any particular
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19 * purpose.
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20 *
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21 * Please cite the author in any work or product based on this material.
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22 *
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23 * ===========================================================================
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24 *
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25 */
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26
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27 /*==========================================================================
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28 * NCBI Generic Fastq Sequence Read Archive schema
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29 */
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30 version 1;
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31
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32 include 'insdc/sra.vschema';
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33 include 'ncbi/sra.vschema';
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34 include 'ncbi/clip.vschema';
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35 include 'ncbi/spotname.vschema';
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36
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37 /* tokenize_spot_name - currently ascii only capability */
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38
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39 extern function NCBI:SRA:spot_name_token
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40 NCBI:SRA:GenericFastq:tokenize_spot_name #1 ( ascii name );
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41
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42 /*--------------------------------------------------------------------------
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43 * NCBI:SRA:GenericFastq:sequence
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44 * Generic Fastq SRA Platform
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45 */
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46 table NCBI:SRA:GenericFastq:sequence #1
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47 = NCBI:SRA:tbl:sra #2.1.3
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48 , NCBI:tbl:base_space #2.0.3
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49 , NCBI:tbl:phred_quality #2.0.4
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50 , NCBI:SRA:tbl:clip #1.0.2
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51 {
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52 ascii platform_name
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53 = < ascii > echo < "UNDEFINED" > ();
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54
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55 INSDC:SRA:platform_id out_platform
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56 = < INSDC:SRA:platform_id > echo < SRA_PLATFORM_UNDEFINED > ();
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57
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58 /* ascii only spot name tokenizer */
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59
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60 NCBI:SRA:spot_name_token out_spot_name_tok
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61 = NCBI:SRA:GenericFastq:tokenize_spot_name ( _out_name );
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62
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63 NCBI:SRA:spot_name_token in_spot_name_tok
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64 = NCBI:SRA:GenericFastq:tokenize_spot_name ( NAME );
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65
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66 /* clips */
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67
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68 physical column < INSDC:coord:one > izip_encoding
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69 .CLIP_ADAPTER_LEFT = CLIP_ADAPTER_LEFT;
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70 physical column < INSDC:coord:one > izip_encoding
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71 .CLIP_ADAPTER_RIGHT = CLIP_ADAPTER_RIGHT;
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72 physical column < INSDC:coord:one > izip_encoding
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73 .CLIP_QUALITY_LEFT = CLIP_QUALITY_LEFT;
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74 physical column < INSDC:coord:one > izip_encoding
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75 .CLIP_QUALITY_RIGHT = CLIP_QUALITY_RIGHT;
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76 }
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77
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78 database NCBI:SRA:GenericFastq:db #1
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79 {
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80 table NCBI:SRA:GenericFastq:sequence #1.0 SEQUENCE;
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81 };
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82
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83 /*--------------------------------------------------------------------------
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84 * NCBI:SRA:GenericFastq:sequence_no_name
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85 * Generic Fastq SRA Platform (without name)
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86 */
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87 table NCBI:SRA:GenericFastq:sequence_no_name #1
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88 = NCBI:SRA:tbl:sra #2.1.3
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89 , NCBI:tbl:base_space #2.0.3
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90 , NCBI:tbl:phred_quality #2.0.4
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91 , NCBI:SRA:tbl:clip #1.0.2
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92 {
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93 ascii platform_name
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94 = < ascii > echo < "UNDEFINED" > ();
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95
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96 INSDC:SRA:platform_id out_platform
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97 = < INSDC:SRA:platform_id > echo < SRA_PLATFORM_UNDEFINED > ();
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98
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99 /* clips */
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100
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101 physical column < INSDC:coord:one > izip_encoding
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102 .CLIP_ADAPTER_LEFT = CLIP_ADAPTER_LEFT;
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103 physical column < INSDC:coord:one > izip_encoding
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104 .CLIP_ADAPTER_RIGHT = CLIP_ADAPTER_RIGHT;
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105 physical column < INSDC:coord:one > izip_encoding
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106 .CLIP_QUALITY_LEFT = CLIP_QUALITY_LEFT;
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107 physical column < INSDC:coord:one > izip_encoding
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108 .CLIP_QUALITY_RIGHT = CLIP_QUALITY_RIGHT;
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109 }
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110
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111 database NCBI:SRA:GenericFastqNoNames:db #1
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112 {
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113 table NCBI:SRA:GenericFastq:sequence_no_name #1.0 SEQUENCE;
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114 };
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115
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116 /*--------------------------------------------------------------------------
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117 * NCBI:SRA:GenericFastq:sequence_log_odds
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118 * Generic Fastq SRA Platform (for log_odds)
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119 */
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120 table NCBI:SRA:GenericFastq:sequence_log_odds #1
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121 = NCBI:SRA:tbl:sra #2.1.3
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122 , NCBI:tbl:base_space #2.0.3
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123 , NCBI:tbl:log_odds_quality #2.1.0
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124 , NCBI:SRA:tbl:clip #1.0.2
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125 {
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126 ascii platform_name
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127 = < ascii > echo < "UNDEFINED" > ();
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128
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129 INSDC:SRA:platform_id out_platform
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130 = < INSDC:SRA:platform_id > echo < SRA_PLATFORM_UNDEFINED > ();
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131
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132 /* ascii only spot name tokenizer */
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133
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134 NCBI:SRA:spot_name_token out_spot_name_tok
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135 = NCBI:SRA:GenericFastq:tokenize_spot_name ( _out_name );
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136
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137 NCBI:SRA:spot_name_token in_spot_name_tok
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138 = NCBI:SRA:GenericFastq:tokenize_spot_name ( NAME );
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139
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140 /* clips */
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141
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142 physical column < INSDC:coord:one > izip_encoding
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143 .CLIP_ADAPTER_LEFT = CLIP_ADAPTER_LEFT;
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144 physical column < INSDC:coord:one > izip_encoding
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145 .CLIP_ADAPTER_RIGHT = CLIP_ADAPTER_RIGHT;
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146 physical column < INSDC:coord:one > izip_encoding
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147 .CLIP_QUALITY_LEFT = CLIP_QUALITY_LEFT;
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148 physical column < INSDC:coord:one > izip_encoding
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149 .CLIP_QUALITY_RIGHT = CLIP_QUALITY_RIGHT;
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150 }
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151
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152 database NCBI:SRA:GenericFastqLogOdds:db #1
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153 {
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154 table NCBI:SRA:GenericFastq:sequence_log_odds #1.0 SEQUENCE;
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155 };
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156
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157 /*--------------------------------------------------------------------------
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158 * NCBI:SRA:GenericFastq:sequence_nanopore
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159 * Oxford Nanopore SRA Platform
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160 */
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161 table NCBI:SRA:GenericFastq:sequence_nanopore #1
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162 = NCBI:SRA:tbl:sra #2.1.3
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163 , NCBI:tbl:base_space #2.0.3
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164 , NCBI:tbl:phred_quality #2.0.4
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165 {
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166 ascii platform_name
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167 = < ascii > echo < "OXFORD_NANOPORE" > ();
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168
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169 INSDC:SRA:platform_id out_platform
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170 = < INSDC:SRA:platform_id > echo < SRA_PLATFORM_OXFORD_NANOPORE > ();
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171
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172 /* ascii only spot name tokenizer */
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173
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174 NCBI:SRA:spot_name_token out_spot_name_tok
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175 = NCBI:SRA:GenericFastq:tokenize_spot_name ( _out_name );
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176
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177 NCBI:SRA:spot_name_token in_spot_name_tok
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178 = NCBI:SRA:GenericFastq:tokenize_spot_name ( NAME );
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179
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180 /* channel and read number columns */
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181
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182 extern column < U32 > izip_encoding #1 CHANNEL;
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183 extern column < U32 > izip_encoding #1 READ_NUMBER;
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184 }
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185
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186 /*--------------------------------------------------------------------------
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187 * NCBI:SRA:GenericFastq:consensus_nanopore
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188 * Oxford Nanopore SRA Platform
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189 */
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190 table NCBI:SRA:GenericFastq:consensus_nanopore #1
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191 = NCBI:SRA:tbl:sra #2.1.3
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192 , NCBI:tbl:base_space #2.0.3
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193 , NCBI:tbl:phred_quality #2.0.4
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194 {
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195 ascii platform_name
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196 = < ascii > echo < "OXFORD_NANOPORE" > ();
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197
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198 INSDC:SRA:platform_id out_platform
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199 = < INSDC:SRA:platform_id > echo < SRA_PLATFORM_OXFORD_NANOPORE > ();
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200
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201 /* ascii only spot name tokenizer */
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202
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203 NCBI:SRA:spot_name_token out_spot_name_tok
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204 = NCBI:SRA:GenericFastq:tokenize_spot_name ( _out_name );
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205
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206 NCBI:SRA:spot_name_token in_spot_name_tok
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207 = NCBI:SRA:GenericFastq:tokenize_spot_name ( NAME );
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208
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209 /* channel and read number columns */
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210
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211 extern column < U32 > izip_encoding #1 CHANNEL;
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212 extern column < U32 > izip_encoding #1 READ_NUMBER;
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213 }
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214
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215 database NCBI:SRA:GenericFastqNanopore:db #1
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216 {
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217 table NCBI:SRA:GenericFastq:sequence_nanopore #1.0 SEQUENCE;
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218 table NCBI:SRA:GenericFastq:consensus_nanopore #1.0 CONSENSUS;
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219 };
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220
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221 database NCBI:SRA:GenericFastqNanoporeConsensusOnly:db #1
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222 {
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223 table NCBI:SRA:GenericFastq:consensus_nanopore #1.0 CONSENSUS;
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224 };
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225
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226 /*--------------------------------------------------------------------------
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227 * NCBI:SRA:GenericFastq:absolid
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228 * Generic fastq for AB Solid platform
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229 */
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230 table NCBI:SRA:GenericFastq:absolid #1
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231 = NCBI:SRA:tbl:sra #2.1.3
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232 , NCBI:tbl:color_space #2.1.0
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233 , NCBI:tbl:phred_quality #2.0.4
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234 , NCBI:SRA:tbl:clip #1.0.2
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235 {
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236 ascii platform_name
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237 = < ascii > echo < "UNDEFINED" > ();
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238
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239 INSDC:SRA:platform_id out_platform
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240 = < INSDC:SRA:platform_id > echo < SRA_PLATFORM_UNDEFINED > ();
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241
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242 /* ascii only spot name tokenizer */
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243
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244 NCBI:SRA:spot_name_token out_spot_name_tok
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245 = NCBI:SRA:GenericFastq:tokenize_spot_name ( _out_name );
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246
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247 NCBI:SRA:spot_name_token in_spot_name_tok
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248 = NCBI:SRA:GenericFastq:tokenize_spot_name ( NAME );
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249
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250 /* clips */
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251
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252 physical column < INSDC:coord:one > izip_encoding
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253 .CLIP_ADAPTER_LEFT = CLIP_ADAPTER_LEFT;
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254 physical column < INSDC:coord:one > izip_encoding
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255 .CLIP_ADAPTER_RIGHT = CLIP_ADAPTER_RIGHT;
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256 physical column < INSDC:coord:one > izip_encoding
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257 .CLIP_QUALITY_LEFT = CLIP_QUALITY_LEFT;
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258 physical column < INSDC:coord:one > izip_encoding
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259 .CLIP_QUALITY_RIGHT = CLIP_QUALITY_RIGHT;
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260 }
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261
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262 database NCBI:SRA:GenericFastqAbsolid:db #1
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263 {
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264 table NCBI:SRA:GenericFastq:absolid #1.0 SEQUENCE;
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265 };