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annotate libs/sratoolkit.2.8.0-centos_linux64/schema/sra/abi.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 ABI 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
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35
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36 /*--------------------------------------------------------------------------
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37 * NCBI:SRA:ABI
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38 * ABI SRA Platform
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39 */
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40
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41 /* tokenize_spot_name
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42 * scans name on input
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43 * tokenizes into parts
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44 */
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45 extern function NCBI:SRA:spot_name_token
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46 NCBI:SRA:ABI:tokenize_spot_name #1 ( ascii name );
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47
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48
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49 /* NCBI:SRA:ABI:common
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50 * basic table interface based upon ABI's pipelines
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51 *
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52 * history:
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53 * 1.0.1 - base explicitly upon changes to sra #1.0.1
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54 * 1.0.2 - base explicitly upon sra #1.0.2
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55 * 1.0.3 - base explicitly upon sra #1.0.3
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56 */
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57 table NCBI:SRA:ABI:common #1.0.3 = INSDC:SRA:tbl:sra #1.0.3
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58 {
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59 // platform name is always 'ABSOLID'
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60 ascii platform_name
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61 = < ascii > echo < "ABSOLID" > ();
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62
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63 /* TRIMMED SEQUENCE
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64 * need to find the 0-based trim_start and trim_len
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65 */
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66 INSDC:coord:zero bio_start = NCBI:SRA:bio_start ( out_read_start, out_read_type );
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67 INSDC:coord:zero trim_start = bio_start;
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68 U32 trim_left = ( U32 ) trim_start;
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69 INSDC:coord:len trim_len = ( INSDC:coord:len ) < U32 > diff ( spot_len, trim_left );
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70
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71 /* COORDINATES
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72 * in addition to X and Y,
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73 * ABI has PANEL
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74 */
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75 column INSDC:coord:val PANEL = out_panel_coord;
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76
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77 // signal
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78 column NCBI:fsamp4 SIGNAL
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79 = out_signal;
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80
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81 NCBI:fsamp4 out_signal = ( NCBI:fsamp4 )
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82 < NCBI:SRA:swapped_fsamp4 > NCBI:SRA:swap ( out_signal_swapped, out_x2cs_bin );
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83
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84
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85 /* INSDC:tbl:sequence inherited productions
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86 * cs_native
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87 * in_cs_key
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88 * out_cs_key
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89 * out_signal_swapped
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90 * out_2cs_bin
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91 * out_2na_bin
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92 * out_4na_bin
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93 * out_dna_text
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94 * out_x2cs_bin
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95 * out_x2na_bin
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96 * in_color_text
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97 * out_2cs_packed
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98 * out_2na_packed
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99 * out_4na_packed
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100 * out_color_text
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101 * out_qual_phred
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102 * out_color_matrix
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103 */
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104
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105 /* INSDC:SRA:tbl:spotname inherited productions
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106 * out_x_coord
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107 * out_y_coord
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108 * out_name_fmt
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109 * out_spot_name
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110 * spot_ids_found
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111 */
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112
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113 /* INSDC:SRA:tbl:spotdesc inherited productions
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114 * out_label
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115 * out_nreads
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116 * out_read_len
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117 * out_label_len
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118 * out_rd_filter
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119 * out_read_type
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120 * out_read_start
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121 * out_label_start
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122 * static_fixed_spot_len
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123 */
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124
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125 /* INSDC:SRA:tbl:stats inherited productions
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126 * base_count
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127 * spot_count
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128 * max_spot_id
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129 * min_spot_id
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130 * in_stats_bin
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131 * bio_base_count
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132 */
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133
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134 /* INSDC:SRA:tbl:sra inherited productions
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135 * out_platform
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136 */
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137
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138 /* NCBI:SRA:ABI:common productions
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139 * out_panel_coord
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140 */
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141 };
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142
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143
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144 /* NCBI:SRA:ABI:tbl:v2 #1
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145 * normalized v2 table
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146 *
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147 * history:
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148 * 1.0.1 - changes to sra #1.0.1
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149 * 1.0.2 - changes to common #1.0.2
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150 * 1.0.3 - sra #2.1.2, color_space #2.0.2, common #1.0.3
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151 * 1.0.4 - updated ancestry
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152 */
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153 physical NCBI:SRA:swapped_fsamp4 NCBI:SRA:ABI:encoding:SIGNAL #2
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154 {
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155 decode { return NCBI:SRA:fsamp4:decode #2 ( @ ); }
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156 encode { return NCBI:SRA:fsamp4:encode #2 < 14, 10 > ( @ ); }
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157 }
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158
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159 table NCBI:SRA:ABI:tbl:v2 #1.0.4
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160 = NCBI:SRA:tbl:sra #2.1.3
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161 , NCBI:tbl:color_space #2.1.0
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162 , NCBI:tbl:phred_quality #2.0.4
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163 , NCBI:SRA:ABI:common #1.0.3
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164 {
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165 /* NAME tokenizing and coordinates
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166 * most work happens in skeyname table
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167 * we still obtain PANEL from name
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168 */
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169 INSDC:coord:val out_panel_coord = ( INSDC:coord:val )
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170 NCBI:SRA:extract_name_coord < NCBI:SRA:name_token:T > ( _out_name, out_spot_name_tok );
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171 NCBI:SRA:spot_name_token out_spot_name_tok
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172 = NCBI:SRA:ABI:tokenize_spot_name ( _out_name );
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173
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174 NCBI:SRA:spot_name_token in_spot_name_tok
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175 = NCBI:SRA:ABI:tokenize_spot_name ( NAME );
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176
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177
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178 /* SIGNAL
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179 * optional, no longer archived
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180 */
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181
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182 // support for individual color inputs
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183 extern column NCBI:fsamp1 FTC
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184 {
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185 read = out_ftc;
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186 validate = < F32 > no_compare #1 ( in_ftc, out_ftc );
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187 }
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188 NCBI:fsamp1 in_ftc = FTC;
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189 NCBI:fsamp1 out_ftc
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190 = ( NCBI:fsamp1 ) < F32 > cut < 0 > ( out_signal );
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191
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192 extern column NCBI:fsamp1 FAM
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193 {
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194 read = out_fam;
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195 validate = < F32 > no_compare #1 ( in_fam, out_fam );
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196 }
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197 NCBI:fsamp1 in_fam = FAM;
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198 NCBI:fsamp1 out_fam
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199 = ( NCBI:fsamp1 ) < F32 > cut < 0 > ( out_signal );
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200
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201 extern column NCBI:fsamp1 CY3
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202 {
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203 read = out_cy3;
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204 validate = < F32 > no_compare #1 ( in_cy3, out_cy3 );
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205 }
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206 NCBI:fsamp1 in_cy3 = CY3;
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207 NCBI:fsamp1 out_cy3
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208 = ( NCBI:fsamp1 ) < F32 > cut < 1 > ( out_signal );
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209
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210 extern column NCBI:fsamp1 TXR
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211 {
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212 read = out_txr;
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213 validate = < F32 > no_compare #1 ( in_txr, out_txr );
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214 }
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215 NCBI:fsamp1 in_txr = TXR;
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216 NCBI:fsamp1 out_txr
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217 = ( NCBI:fsamp1 ) < F32 > cut < 2 > ( out_signal );
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218
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219 extern column NCBI:fsamp1 CY5
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220 {
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221 read = out_cy5;
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222 validate = < F32 > no_compare #1 ( in_cy5, out_cy5 );
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223 }
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224 NCBI:fsamp1 in_cy5 = CY5;
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225 NCBI:fsamp1 out_cy5
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226 = ( NCBI:fsamp1 ) < F32 > cut < 3 > ( out_signal );
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227
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228 // intermediate input (writing) production
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229 NCBI:fsamp4 in_signal
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230 = SIGNAL
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231 | ( NCBI:fsamp4 ) < F32 > paste ( in_ftc, in_cy3, in_txr, in_cy5 )
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232 | ( NCBI:fsamp4 ) < F32 > paste ( in_fam, in_cy3, in_txr, in_cy5 );
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233
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234 // overridden output production
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235 NCBI:SRA:swapped_fsamp4 out_signal_swapped = .SIGNAL;
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236
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237 // rule for writing SIGNAL
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238 physical column NCBI:SRA:ABI:encoding:SIGNAL #2 .SIGNAL
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239 = ( NCBI:SRA:swapped_fsamp4 ) < NCBI:fsamp4 > NCBI:SRA:swap ( in_signal, in_x2cs_bin )
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240 | ( NCBI:SRA:swapped_fsamp4 ) < NCBI:fsamp4 > NCBI:SRA:swap ( in_signal, in_2cs_bin );
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241 };