annotate format_versionning.MD @ 1:1c2ce385b84e draft

" master branch Updating"
author lain
date Tue, 24 Nov 2020 18:57:10 +0000
parents a174cbbb12dd
children 2937e72e5891
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
1
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
2 INTRODUCTION
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
3 =====
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
4 This file describes the format of the database generated by XSeeker
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
5 Preprocessor. This format will evolve in the future to fit users
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
6 wanted features. That's why there is a history of versions numbers,
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
7 describing what they brought to the sqlite file, and how it was usefull.
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
8
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
9 The first version (the older one) is at the bottom of this file, and the
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
10 modifications provided by the newest versions are on top of the file.
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
11
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
12
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
13 VERSION 1.1.2
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
14 =====
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
15 add missing mz_tab_info$group_length field to produce mzTab
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
16
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
17 VERSION 1.1.1
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
18 =====
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
19 add missing mz_tab_info$dataset_path field to produce mzTab
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
20
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
21
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
22 VERSION 1.1.0
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
23 =====
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
24 Summary:
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
25 - The field `mz_tab_info` was added in new table smol_xcms_set.
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
26
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
27 smol_xcms_set table added
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
28 -----
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
29 This table contains a subset of the original ms file.
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
30
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
31 mz_tab_info field added to smol_xcms_set
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
32 -----
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
33 This field contains five subfields:
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
34 - sampclass ;
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
35 - sampnames ;
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
36 - rtmed ;
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
37 - mzmed ;
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
38 - smallmolecule_abundance_assay .
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
39
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
40 These fields were added after users asked to export data from XSeeker
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
41 in mzTab files.
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
42 XCMS has some functions to extract sampclass, sampnames, rtmed, mzmed
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
43 and smallmolecule_abundance_assay from xcms set. Then, they are used
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
44 in the mz tab creation process, but we didn't want to keep the whole
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
45 xcmsset object. So we used the original code from XCMS and modified it
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
46 a little bit, justifying the extraction of these new fields.
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
47
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
48
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
49 VERSION 1.0.0
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
50 =====
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
51
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
52
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
53 DATABASE
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
54 -----
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
55
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
56 ### SAMPLE
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
57
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
58 #### RAW
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
59 This structure is an epurated and enriched version of the original
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
60 rdata, saved as a compressed env:
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
61 `blob::blob(fst::compress_fst(serialize(raw, NULL), compression=100))`
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
62
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
63 The fields contained in the env are as follow:
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
64
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
65 ##### variableMetadata
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
66
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
67 ##### tic
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
68
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
69 ##### mz
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
70
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
71 ##### scanindex
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
72
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
73 ##### scantime
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
74
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
75 ##### intensity
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
76
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
77 ##### polarity
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
78
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
79 ##### sample_name
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
80
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
81 ##### dataset_path
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
82
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
83 ##### process_params
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
84
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
85 ##### enriched_rdata
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
86
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
87 ##### enriched_rdata_version
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
88
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
89 ##### tool_name
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
90
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
91 ##### enriched_rdata_doc