annotate libs/sratoolkit.2.8.0-centos_linux64/schema/sra/helicos.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 Helicos 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 * functions
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38 */
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39
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40 /* tokenize_spot_name
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41 * scans name on input
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42 * tokenizes into parts
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43 */
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44 extern function NCBI:SRA:spot_name_token
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45 NCBI:SRA:Helicos:tokenize_spot_name #1 ( ascii name );
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46
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47
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48 /* Helicos:tbl
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49 *
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50 * history:
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51 * 1.0.1 - explictly base upon ancestry
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52 * 1.0.2 - base explicitly upon latest ancestry
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53 * 1.0.3 - base explicitly upon latest ancestry
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54 * 1.0.4 - base explicitly upon latest ancestry
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55 */
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56 table NCBI:SRA:Helicos:tbl:v2 #1.0.4
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57 = NCBI:SRA:tbl:sra #2.1.3
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58 , NCBI:tbl:base_space #2.0.3
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59 , NCBI:tbl:phred_quality #2.0.3
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60 {
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61 ascii platform_name
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62 = < ascii > echo < "HELICOS" > ();
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63
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64 /* NAME tokenizing and coordinates
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65 * most work happens in skeyname table
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66 * we still obtain REGION from name
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67 */
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68
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69 readonly column INSDC:coord:val CHANNEL = ( INSDC:coord:val )
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70 NCBI:SRA:extract_name_coord < NCBI:SRA:name_token:L > ( _out_name, out_spot_name_tok );
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71 readonly column INSDC:coord:val FIELD = ( INSDC:coord:val )
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72 NCBI:SRA:extract_name_coord < NCBI:SRA:name_token:T > ( _out_name, out_spot_name_tok );
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73 NCBI:SRA:spot_name_token out_spot_name_tok
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74 = NCBI:SRA:Helicos:tokenize_spot_name ( _out_name );
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75
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76 readonly column INSDC:coord:val CAMERA = out_x_coord;
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77 readonly column INSDC:coord:val POS = out_y_coord;
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78
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79 NCBI:SRA:spot_name_token in_spot_name_tok
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80 = NCBI:SRA:Helicos:tokenize_spot_name ( NAME );
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81
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82 INSDC:coord:zero trim_start
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83 = < INSDC:coord:zero > echo < 0 > ();
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84 INSDC:coord:len trim_len = spot_len;
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85 };