Mercurial > repos > fgiacomoni > xseekerpreparator
diff format_versionning.MD @ 0:1660665c081e draft
#issue9 branch Updating - - Fxx
author | fgiacomoni |
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date | Thu, 19 Nov 2020 14:28:46 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/format_versionning.MD Thu Nov 19 14:28:46 2020 +0000 @@ -0,0 +1,91 @@ + +INTRODUCTION +===== +This file describes the format of the database generated by XSeeker +Preprocessor. This format will evolve in the future to fit users +wanted features. That's why there is a history of versions numbers, +describing what they brought to the sqlite file, and how it was usefull. + +The first version (the older one) is at the bottom of this file, and the +modifications provided by the newest versions are on top of the file. + + +VERSION 1.1.2 +===== +add missing mz_tab_info$group_length field to produce mzTab + +VERSION 1.1.1 +===== +add missing mz_tab_info$dataset_path field to produce mzTab + + +VERSION 1.1.0 +===== +Summary: + - The field `mz_tab_info` was added in new table smol_xcms_set. + +smol_xcms_set table added +----- +This table contains a subset of the original ms file. + +mz_tab_info field added to smol_xcms_set +----- +This field contains five subfields: + - sampclass ; + - sampnames ; + - rtmed ; + - mzmed ; + - smallmolecule_abundance_assay . + +These fields were added after users asked to export data from XSeeker +in mzTab files. +XCMS has some functions to extract sampclass, sampnames, rtmed, mzmed +and smallmolecule_abundance_assay from xcms set. Then, they are used +in the mz tab creation process, but we didn't want to keep the whole +xcmsset object. So we used the original code from XCMS and modified it +a little bit, justifying the extraction of these new fields. + + +VERSION 1.0.0 +===== + + +DATABASE +----- + +### SAMPLE + +#### RAW +This structure is an epurated and enriched version of the original +rdata, saved as a compressed env: +`blob::blob(fst::compress_fst(serialize(raw, NULL), compression=100))` + +The fields contained in the env are as follow: + +##### variableMetadata + +##### tic + +##### mz + +##### scanindex + +##### scantime + +##### intensity + +##### polarity + +##### sample_name + +##### dataset_path + +##### process_params + +##### enriched_rdata + +##### enriched_rdata_version + +##### tool_name + +##### enriched_rdata_doc \ No newline at end of file