Mercurial > repos > charles_s_test > seqsero2

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
author charles_s_test
date Mon, 27 Nov 2017 11:21:07 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
1 /*===========================================================================
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
2 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
3 * PUBLIC DOMAIN NOTICE
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
4 * National Center for Biotechnology Information
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
5 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
6 * This software/database is a "United States Government Work" under the
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
7 * terms of the United States Copyright Act. It was written as part of
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
8 * the author's official duties as a United States Government employee and
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
9 * thus cannot be copyrighted. This software/database is freely available
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
10 * to the public for use. The National Library of Medicine and the U.S.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
11 * Government have not placed any restriction on its use or reproduction.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
12 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
13 * Although all reasonable efforts have been taken to ensure the accuracy
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
14 * and reliability of the software and data, the NLM and the U.S.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
15 * Government do not and cannot warrant the performance or results that
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
16 * may be obtained by using this software or data. The NLM and the U.S.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
17 * Government disclaim all warranties, express or implied, including
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
18 * warranties of performance, merchantability or fitness for any particular
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
19 * purpose.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
20 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
21 * Please cite the author in any work or product based on this material.
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
22 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
23 * ===========================================================================
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
24 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
25 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
26
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
27 /*==========================================================================
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
28 * NCBI Ion Torrent Sequence Read Archive schema
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
29 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
30 version 1;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
31
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
32 include 'ncbi/sra.vschema';
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
33 include 'ncbi/spotname.vschema';
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
34 include 'ncbi/clip.vschema';
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
35
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
36
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
37 /*--------------------------------------------------------------------------
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
38 * functions
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
39 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
40
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
41
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
42 /* tokenize_spot_name
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
43 * scans name on input
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
44 * tokenizes into parts
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
45 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
46 extern function NCBI:SRA:spot_name_token
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
47 NCBI:SRA:IonTorrent:tokenize_spot_name #1 ( ascii name );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
48
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
49
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
50 /*--------------------------------------------------------------------------
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
51 * table
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
52 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
53
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
54 physical INSDC:position:one NCBI:SRA:IonTorrent:encoding:POSITION #1
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
55 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
56 decode
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
57 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
58 I32 pos_1st_deriv = iunzip ( @ );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
59 return ( INSDC:position:one ) < I32 > integral ( pos_1st_deriv );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
60 }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
61 encode
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
62 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
63 I32 pos_1st_deriv = < I32 > deriv ( @ );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
64 return izip ( pos_1st_deriv );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
65 }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
66 }
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
67
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
68 /* IonTorrent:tbl
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
69 *
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
70 * history:
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
71 * 1.0.1 - updated ancestry
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
72 * 1.0.2 - updated ancestry
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
73 * 1.0.3 - updated ancestry
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
74 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
75 table NCBI:SRA:IonTorrent:tbl:v2 #1.0.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
76 = INSDC:SRA:tbl:sra #1.0.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
77 , NCBI:SRA:tbl:sra_nopos #2.1.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
78 , NCBI:tbl:base_space #2.0.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
79 , NCBI:tbl:phred_quality #2.0.3
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
80 , NCBI:SRA:tbl:clip #1.0.2
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
81 {
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
82 /* PLATFORM is always ION_TORRENT */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
83 ascii platform_name
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
84 = < ascii > echo < "ION_TORRENT" > ();
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
85
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
86 /* NAME tokenizing and coordinates
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
87 * most work happens in skeyname table
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
88 */
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
89 NCBI:SRA:spot_name_token out_spot_name_tok
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
90 = NCBI:SRA:IonTorrent:tokenize_spot_name ( _out_name );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
91
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
92 NCBI:SRA:spot_name_token in_spot_name_tok
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
93 = NCBI:SRA:IonTorrent:tokenize_spot_name ( NAME );
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
94
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
95 // special sequences
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
96 column < INSDC:dna:text > zip_encoding FLOW_CHARS;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
97 column < INSDC:dna:text > zip_encoding KEY_SEQUENCE;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
98
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
99 // position stored as normal 1-based coordinate
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
100 INSDC:position:one out_position = .POSITION;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
101 physical column NCBI:SRA:IonTorrent:encoding:POSITION
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
102 .POSITION = POSITION;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
103
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
104
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
105 // clips
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
106 physical column < INSDC:coord:one > izip_encoding
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
107 .CLIP_ADAPTER_LEFT = CLIP_ADAPTER_LEFT;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
108 physical column < INSDC:coord:one > izip_encoding
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
109 .CLIP_ADAPTER_RIGHT = CLIP_ADAPTER_RIGHT;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
110 physical column < INSDC:coord:one > izip_encoding
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
111 .CLIP_QUALITY_LEFT = CLIP_QUALITY_LEFT;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
112 physical column < INSDC:coord:one > izip_encoding
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
113 .CLIP_QUALITY_RIGHT = CLIP_QUALITY_RIGHT;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
114
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
115 // signal
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
116 column < NCBI:isamp1 > izip_encoding SIGNAL;
38ad1130d077 planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
diff changeset
117 };