Pride submission prep #43
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added 25 commits
March 9, 2023 10:35
- save some intermediate files - visualize some stats
- prepare upload to pride (which unified and annonymized identifiers)
- data curation - allow selection of raw data
- only load intensities - transpose and create mask view in separate document - dump counts for samples and features
- create machine specific subfolders for pride - instrument_name added for subfolders
- don't support long data for now - skip categorical data checking keep old code as comments for now (as a reminder)
- was at some point used to investigate which data to use
- notebook is for exploration of single MaxQuant folder
- erda notebooks create dumps which are then processed in "hela" notebooks - rename and describe
- create folder and put commands for raw files - use -f for using commands read from a file with lftp - start uploading
- sanity checks and upload missing or incomplete files - rename sample names in MQ output
technology type -> indicates that it is not RNA (MAGE-TAB format)
- all 7444 selected files for upload are used to create unified dums - small plotting improvements and minor other changes
- check all files are in list of files (queried from server) - create some dummy files (placeholders) locally for pride submission tool - manuelly annotate the submission.px text file from the submission tool (basically: add files) - 🐛 SDRF file had ontology issues (and cellline template was not enough)
- plots based on metadata
- metadata is provided on pride ("pride_metadata.csv")
Splitted metadata creation from analysis
- relevant information of mq_summaries.csv also provided in metadata_pride.csv
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Pride data release preparation.
pride submission scripts ->
00_0_*.ipynbupdate erda (FTP server) notebooks, build dumps for pride of 7,444 selected files ->
erda_*.ipynbadd python version of notebooks for better diffs in the future