Mercurial > repos > charles_s_test > seqsero2

annotate libs/sratoolkit.2.8.0-centos_linux64/schema/insdc/seq.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 * Sequence schema
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29 */
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30 version 1;
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31
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32 include 'vdb/vdb.vschema';
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33 include 'insdc/insdc.vschema';
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34
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35
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36 /*--------------------------------------------------------------------------
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37 * rand_4na_2na
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38 * converts 4na to 2na
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39 *
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40 * substitutes a random base for ambiguities
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41 * from the bases allowed in the 4na.
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42 *
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43 * A | C | G | T
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44 * =================
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45 * N | | | # any base may be substituted
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46 * A * | | | # always A
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47 * C | * | | # always C
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48 * M * | * | | # A or C
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49 * G | | * | # always G
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50 * R * | | * | # A or G
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51 * S | * | * | # C or G
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52 * V * | * | * | # A, C or G
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53 * T | | | * # always T
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54 * W * | | | * # A or T
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55 * Y | * | | * # C or T
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56 * H * | * | | * # A, C or T
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57 * K | | * | * # G or T
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58 * D * | | * | * # A, G or T
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59 * B | * | * | * # C, G or T
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60 * N * | * | * | * # any base may be substituted
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61 */
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62 extern function
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63 INSDC:2na:bin INSDC:SEQ:rand_4na_2na #1 ( INSDC:4na:bin rd_bin );
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64
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65
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66 /*--------------------------------------------------------------------------
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67 * sequence
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68 * basic sequence table
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69 *
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70 * history:
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71 * 1.0.1 - introduced text-mode QUALITY columns
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72 */
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73 table INSDC:tbl:sequence #1.0.1
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74 {
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75 /* READ
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76 * native or converted DNA sequence
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77 */
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78
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79 // default is IUPAC character representation
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80 extern default column INSDC:dna:text READ
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81 {
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82 read = out_dna_text;
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83 validate = < INSDC:dna:text > compare ( in_dna_text, out_dna_text );
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84 }
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85
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86 // 4na representation - unpacked and packed
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87 extern column INSDC:4na:bin READ = out_4na_bin;
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88 extern column INSDC:4na:packed READ = out_4na_packed;
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89
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90 // x2na representation - 2na with ambiguity
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91 extern column INSDC:x2na:bin READ = out_x2na_bin;
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92
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93 // 2na representation - 2na with no ambiguity - unpacked and packed
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94 extern column INSDC:2na:bin READ = out_2na_bin;
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95 extern column INSDC:2na:packed READ = out_2na_packed;
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96
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97
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98
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99 /* CSREAD
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100 * native or converted color-space sequence
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101 */
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102
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103 // default is ASCII character representation
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104 extern default column INSDC:color:text CSREAD
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105 {
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106 read = out_color_text;
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107 validate = < INSDC:color:text > compare ( in_color_text, out_color_text );
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108 }
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109
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110 // x2cs representation - 2cs with ambiguity
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111 extern column INSDC:x2cs:bin CSREAD = out_x2cs_bin;
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112
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113 // 2cs representation - 2cs with no ambiguity - unpacked and packed
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114 extern column INSDC:2cs:bin CSREAD = out_2cs_bin;
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115 extern column INSDC:2cs:packed CSREAD = out_2cs_packed;
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116
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117 /* CS_NATIVE
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118 * is color-space the native sequence space
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119 */
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120 readonly column bool CS_NATIVE = cs_native;
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121
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122 /* CS_KEY
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123 * leading call given in base-space
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124 */
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125 extern column INSDC:dna:text CS_KEY
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126 {
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127 read = out_cs_key;
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128 validate = < INSDC:dna:text > compare ( in_cs_key, out_cs_key );
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129 }
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130
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131 /* COLOR_MATRIX
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132 * matrix used for color-space conversions
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133 */
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134 extern column U8 COLOR_MATRIX = out_color_matrix;
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135
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136
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137 /* QUALITY
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138 * base or color call qualities
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139 */
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140
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141 // PHRED is default
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142 extern default column INSDC:quality:phred QUALITY = out_qual_phred;
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143
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144 // textual encodings
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145 extern column INSDC:quality:text:phred_33 QUALITY
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146 = out_qual_text_phred_33
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147 | ( INSDC:quality:text:phred_33 ) < B8 > sum < 33 > ( out_qual_phred );
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148 extern column INSDC:quality:text:phred_64 QUALITY
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149 = out_qual_text_phred_64
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150 | ( INSDC:quality:text:phred_64 ) < B8 > sum < 64 > ( out_qual_phred );
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151
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152
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153 /* SIGNAL
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154 * signal and intensity information is unspecified
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155 */
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156 INSDC:coord:len signal_len
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157 = ( INSDC:coord:len ) row_len ( out_signal )
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158 | < INSDC:coord:len > echo < 0 > ();
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159
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160
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161 /* VIRTUAL PRODUCTIONS
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162 * cs_native
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163 * in_cs_key
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164 * out_cs_key
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165 * out_signal
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166 * in_dna_text
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167 * out_2cs_bin
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168 * out_2na_bin
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169 * out_4na_bin
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170 * out_dna_text
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171 * out_x2cs_bin
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172 * out_x2na_bin
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173 * in_color_text
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174 * out_2cs_packed
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175 * out_2na_packed
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176 * out_4na_packed
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177 * out_color_text
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178 * out_qual_phred
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179 * out_color_matrix
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180 */
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181 };
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182
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183
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184 /*--------------------------------------------------------------------------
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185 * protein
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186 * basic protein sequence table
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187 */
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188 table INSDC:tbl:protein #1
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189 {
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190 /* PROTEIN
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191 * native or converted protein sequence
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192 */
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193
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194 // default is IUPAC character representation
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195 extern default column INSDC:protein:text PROTEIN
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196 {
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197 read = out_protein_text;
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198 validate = < INSDC:protein:text > compare ( in_protein_text, out_protein_text );
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199 }
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200
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201 // aa representation
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202 extern column INSDC:aa:bin PROTEIN = out_aa_bin;
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203
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204
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205 /* INSDC:tbl:protein productions
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206 * out_aa_bin
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207 * in_protein_text
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208 * out_protein_text
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209 */
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210 };