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annotate libs/sratoolkit.2.8.0-centos_linux64/schema/sra/454.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 454 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 'ncbi/sra.vschema';
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33 include 'ncbi/spotname.vschema';
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34 include 'ncbi/clip.vschema';
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35
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36
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37 /*--------------------------------------------------------------------------
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38 * functions
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39 */
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40
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41 /* dynamic_read_desc
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42 * uses inputs to determine read type and segmentation
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43 *
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44 * "edit_distance" [ CONST, OPTIONAL ] - a tolerance figure for
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45 * linker matching, where 0 requires exact match, 5 is default.
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46 *
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47 * "spot" [ DATA ] - bases for entire spot
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48 *
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49 * "key" [ DATA, CONTROL ] - bases for key sequence. for version 1,
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50 * the first base following key is taken as biological start
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51 *
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52 * "linker" [ DATA, CONTROL, OPTIONAL ] - if present, is used to separate
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53 * all bases following "key" into mate pair biological reads
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54 *
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55 * returns a trio for each identified read, with read type, start and length
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56 */
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57 typeset NCBI:SRA:_454_:drdparam_set { ascii, U8, INSDC:2na:packed };
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58 extern function
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59 U32 [ 3 ] NCBI:SRA:_454_:dynamic_read_desc #1 < * U32 edit_distance >
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60 ( NCBI:SRA:_454_:drdparam_set spot, NCBI:SRA:_454_:drdparam_set key
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61 * NCBI:SRA:_454_:drdparam_set linker );
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62
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63 const U32 NCBI:SRA:_454_:dyn_read_type = 0;
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64 const U32 NCBI:SRA:_454_:dyn_read_start = 1;
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65 const U32 NCBI:SRA:_454_:dyn_read_len = 2;
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66
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67
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68 /* tokenize_spot_name
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69 * scans name on input
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70 * tokenizes into parts
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71 */
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72 extern function NCBI:SRA:spot_name_token
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73 NCBI:SRA:_454_:tokenize_spot_name #1 ( ascii name );
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74
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75
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76 /*--------------------------------------------------------------------------
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77 * NCBI:SRA:_454_:common
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78 * Roche 454 SRA Platform
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79 *
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80 * history:
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81 * 1.0.1 - explictly base upon sra #1.0.1
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82 * 1.0.2 - bring in clip processing from external table
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83 * 1.0.3 - base explicitly upon sra #1.0.2, clip #1.0.1
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84 * 1.0.4 - base explicitly upon sra #1.0.3, clip #1.0.2
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85 */
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86 table NCBI:SRA:_454_:common #1.0.4 = INSDC:SRA:tbl:sra #1.0.3, NCBI:SRA:tbl:clip #1.0.2
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87 {
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88 /* PLATFORM
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89 * platform name is always 454
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90 */
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91 ascii platform_name
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92 = < ascii > echo < "454" > ();
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93
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94 /* 454 TECHNICAL SEQUENCES
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95 */
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96 column INSDC:dna:text FLOW_CHARS = out_flow_chars;
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97 INSDC:dna:text in_flow_chars
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98 = < INSDC:dna:text, INSDC:dna:text > map < 'acgtn.', 'ACGTNN' > ( FLOW_CHARS );
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99 column INSDC:dna:text KEY_SEQUENCE = out_key_sequence;
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100 INSDC:dna:text in_key_sequence
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101 = < INSDC:dna:text, INSDC:dna:text > map < 'acgtn.', 'ACGTNN' > ( KEY_SEQUENCE );
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102 column INSDC:dna:text LINKER_SEQUENCE = out_linker_sequence;
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103 INSDC:dna:text in_linker_sequence
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104 = < INSDC:dna:text, INSDC:dna:text > map < 'acgtn.', 'ACGTNN' > ( LINKER_SEQUENCE );
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105
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106 // binary technical sequences
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107 INSDC:x2na:bin out_flow_bin
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108 = < INSDC:dna:text, INSDC:x2na:bin > map < INSDC:x2na:map:CHARSET, INSDC:x2na:map:BINSET > ( out_flow_chars );
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109 INSDC:x2na:bin out_key_bin
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110 = < INSDC:dna:text, INSDC:x2na:bin > map < INSDC:x2na:map:CHARSET, INSDC:x2na:map:BINSET > ( out_key_sequence );
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111 INSDC:x2na:bin out_linker_bin
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112 = < INSDC:dna:text, INSDC:x2na:bin > map < INSDC:x2na:map:CHARSET, INSDC:x2na:map:BINSET > ( out_linker_sequence );
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113
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114 /* SIGNAL
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115 * single channel integer
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116 */
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117 column NCBI:isamp1 SIGNAL = out_signal;
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118 NCBI:isamp1 out_signal = .SIGNAL;
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119
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120
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121 /* INSDC:tbl:sequence inherited productions
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122 * cs_native
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123 * out_cs_key
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124 * in_dna_text
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125 * out_2cs_bin
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126 * out_2na_bin
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127 * out_4na_bin
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128 * out_dna_text
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129 * out_x2cs_bin
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130 * out_x2na_bin
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131 * out_2cs_packed
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132 * out_2na_packed
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133 * out_4na_packed
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134 * out_color_text
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135 * out_qual_phred
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136 * out_color_matrix
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137 */
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138
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139 /* INSDC:SRA:tbl:spotname inherited productions
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140 * out_x_coord
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141 * out_y_coord
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142 * out_name_fmt
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143 * out_spot_name
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144 * spot_ids_found
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145 */
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146
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147 /* INSDC:SRA:tbl:spotdesc inherited productions
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148 * trim_len
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149 * out_label
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150 * out_nreads
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151 * trim_start
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152 * out_read_len
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153 * out_label_len
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154 * out_rd_filter
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155 * out_read_type
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156 * out_read_start
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157 * out_label_start
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158 * static_fixed_spot_len
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159 */
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160
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161 /* INSDC:SRA:tbl:stats inherited productions
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162 * base_count
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163 * spot_count
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164 * max_spot_id
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165 * min_spot_id
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166 * in_stats_bin
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167 * bio_base_count
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168 */
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169
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170 /* NCBI:tbl:n_encoding inherited productions
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171 * read_unpack
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172 */
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173
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174 /* NCBI:SRA:_454_:common productions
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175 * .SIGNAL
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176 * .CLIP_ADAPTER_LEFT
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177 * .CLIP_QUALITY_LEFT
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178 * .CLIP_ADAPTER_RIGHT
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179 * .CLIP_QUALITY_RIGHT
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180 * out_flow_chars
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181 * out_key_sequence
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182 * out_linker_sequence
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183 */
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184 };
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185
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186
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187 /*--------------------------------------------------------------------------
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188 * NCBI:SRA:_454_:tbl:v2
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189 * Roche 454 SRA Platform
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190 *
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191 * history:
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192 * 1.0.1 - explictly base upon sra #1.0.1 and related changes
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193 * 1.0.2 - respond to change to 454:common base table #1.0.2
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194 */
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195
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196 // encodings are declared to have their own version
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197 // so that they may be changed over time independently
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198 physical INSDC:coord:one NCBI:SRA:_454_:encoding:CLIP #2
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199 {
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200 decode { return ( INSDC:coord:one ) iunzip ( @ ); }
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201 encode { return izip ( @ ); }
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202 }
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203
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204 physical NCBI:isamp1 NCBI:SRA:_454_:encoding:SIGNAL #2
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205 {
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206 decode { return ( NCBI:isamp1 ) iunzip ( @ ); }
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207 encode { return izip ( @ ); }
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208 }
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209
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210 physical INSDC:position:one NCBI:SRA:_454_:encoding:POSITION #2
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211 {
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212 decode
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213 {
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214 I32 pos_1st_deriv = iunzip ( @ );
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215 return ( INSDC:position:one ) < I32 > integral ( pos_1st_deriv );
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216 }
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217 encode
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218 {
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219 I32 pos_1st_deriv = < I32 > deriv ( @ );
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220 return izip ( pos_1st_deriv );
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221 }
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222 }
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223
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224 /* normalized v2 table
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225 *
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226 * history:
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227 * 1.0.6 - base upon updated ancestry
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228 * 1.0.7 - base upon updated ancestry
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229 */
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230 table NCBI:SRA:_454_:tbl:v2 #1.0.7
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231 = NCBI:SRA:tbl:sra_nopos #2.1.3
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232 , NCBI:tbl:base_space #2.0.3
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233 , NCBI:tbl:phred_quality #2.0.3
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234 , NCBI:SRA:_454_:common #1.0.4
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235 {
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236 /* NAME tokenizing and coordinates
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237 * most work happens in skeyname table
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238 * we still obtain REGION from name
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239 */
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240 readonly column INSDC:coord:val REGION = ( INSDC:coord:val )
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241 NCBI:SRA:extract_name_coord < NCBI:SRA:name_token:T > ( _out_name, out_spot_name_tok );
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242 NCBI:SRA:spot_name_token out_spot_name_tok
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243 = NCBI:SRA:_454_:tokenize_spot_name ( _out_name );
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244
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245 NCBI:SRA:spot_name_token in_spot_name_tok
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246 = NCBI:SRA:_454_:tokenize_spot_name ( NAME );
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247
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248 // special sequences
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249 INSDC:dna:text out_flow_chars
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250 = .FLOW_CHARS
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251 | < INSDC:dna:text > echo < 'TACG' > ( .SIGNAL )
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252 | < INSDC:dna:text > echo < 'TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACG' > ();
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253
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254 physical column < INSDC:dna:text > zip_encoding
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255 .FLOW_CHARS = in_flow_chars;
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256
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257 INSDC:dna:text out_key_sequence
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258 = .KEY_SEQUENCE
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259 | < INSDC:dna:text > echo < 'TCAG' > ();
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260
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261 physical column < INSDC:dna:text > zip_encoding
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262 .KEY_SEQUENCE = in_key_sequence;
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263
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264 INSDC:dna:text out_linker_sequence = .LINKER_SEQUENCE;
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265 physical column < INSDC:dna:text > zip_encoding
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266 .LINKER_SEQUENCE = in_linker_sequence;
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267
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268 // linker needs to be representable by its own table
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269 // either in metadata or somewhere else
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270
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271 // position stored as normal 1-based coordinate
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272 INSDC:position:one out_position = .POSITION;
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273 physical column NCBI:SRA:_454_:encoding:POSITION #2
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274 .POSITION = POSITION;
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275
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276 // clips
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277 physical column NCBI:SRA:_454_:encoding:CLIP #2
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278 .CLIP_ADAPTER_LEFT = CLIP_ADAPTER_LEFT;
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279 physical column NCBI:SRA:_454_:encoding:CLIP #2
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280 .CLIP_ADAPTER_RIGHT = CLIP_ADAPTER_RIGHT;
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281 physical column NCBI:SRA:_454_:encoding:CLIP #2
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282 .CLIP_QUALITY_LEFT = CLIP_QUALITY_LEFT;
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283 physical column NCBI:SRA:_454_:encoding:CLIP #2
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284 .CLIP_QUALITY_RIGHT = CLIP_QUALITY_RIGHT;
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285
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286 // signal
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287 physical column NCBI:SRA:_454_:encoding:SIGNAL #2
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288 .SIGNAL = SIGNAL;
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289 };