[WIP] Examples dataset for Phenotype BEP#393
[WIP] Examples dataset for Phenotype BEP#393Remi-Gau wants to merge 2 commits intobids-standard:masterfrom
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| """Utility script to remove subjects from the phenotype dataset. | |||
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| """Utility script to remove subjects from the phenotype dataset. | |
| """ | |
| Utility script to remove subjects from the phenotype dataset. |
| if "sub-ON01016" not in subjects_to_keep: | ||
| subjects_to_keep.append('sub-ON01016') |
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Please comment for reasoning?
| print(f'Removing {subject_dir}') | ||
| shutil.rmtree(subject_dir) | ||
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| # remove subject from participants.tsv |
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| # remove subject from participants.tsv | |
| # remove subjects from participants.tsv |
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by the way I am not sure we will want to keep the script in the end, but I put it in the PR in case we want to regenerate those datasets slightly differently |
| print(participants_df) | ||
| participants_df.to_csv(participants_tsv, sep='\t', index=False) | ||
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| # remove subject from all tsv in phenotype folder |
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| # remove subject from all tsv in phenotype folder | |
| # remove subjects from all tsv's in phenotype folder |
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What a great utility! Thanks.
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Maybe delete the unpaired JSONs like this one (meaning there's no TSV to go with the JSON)?
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yes I think I did that manually for a couple of things and that would have to be scripted.
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another todo in the scrip:
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| participant_id bai01_r03, bai1_1 bai02_r03, bai1_2 bai03_r03, bai1_3 bai04_r03, bai1_4 bai05_r03, bai1_5 bai06_r03, bai1_6 bai07_r03, bai2_7 bai08_r03, bai2_8 bai09_r03, bai2_9 bai10_r03, bai2_10 bai11_r03, bai2_11 bai12_r03, bai3_12 bai13_r03, bai3_13 bai14_r03, bai3_14 bai15_r03, bai3_15 bai16_r03, bai3_16 bai17_r03, bai4_1 bai18_r03, bai4_2 bai19_r03, bai4_3 bai20_r03, bai4_4 bai21_r03, bai4_5 | |||
| sub-ON66199 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 | |||
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I can't remember if we decided since this file is nested under a participant_id folder that we don't need the participant_id column, or if maybe it just always needs to be there. Open to commentary...
ericearl
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What a wonderful bunch of examples and utilities! Address those few mini-suggestions and the couple slightly larger comments and I approve!
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Out of date with the BEP as it currently stands. Can reopen if this needs revisiting. |
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This PR has been superseded by #465 based on updates to the phenotypic spec. |
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