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extract_all.sh
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34 lines (26 loc) · 4.67 KB
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#!/usr/bin/env bash
# Note that this script is not supposed to be run on any other computer than jontejj's
# as it depends on large output.mrd files not version controlled.
# It's only included to show the general idea of how the dataset .pkl files were created
set -euxo pipefail
python mirdeepsquared/extract_features.py /Volumes/Mac/Users/jonatanjoensson/school/molecular-biology/mirdeep2-data/TCGA-LUSC/result_19_01_2023_t_23_35_49.csv /Volumes/Mac/Users/jonatanjoensson/school/molecular-biology/mirdeep2-data/TCGA-LUSC/output.mrd resources/dataset/true_positives/true_positives_TCGA_LUSC_all.pkl -tp --section known
python mirdeepsquared/mirgene_db_filter.py resources/dataset/true_positives/true_positives_TCGA_LUSC_all.pkl resources/ALL-precursors_in_mirgene_db.fas resources/dataset/true_positives_TCGA_LUSC_only_precursors_in_mirgene_db.pkl --stringent
python mirdeepsquared/extract_features.py /Volumes/Mac/Users/jonatanjoensson/school/molecular-biology/mirdeep2-data/TCGA-BRCA/result_30_12_2022_t_12_51_40.csv /Volumes/Mac/Users/jonatanjoensson/school/molecular-biology/mirdeep2-data/TCGA-BRCA/TCGA-BRCA-output.mrd resources/dataset/true_positives/true_positives_TCGA_BRCA.pkl -tp --section known
python mirdeepsquared/mirgene_db_filter.py resources/dataset/true_positives/true_positives_TCGA_BRCA.pkl resources/ALL-precursors_in_mirgene_db.fas resources/dataset/true_positives_TCGA_BRCA_only_precursors_in_mirgene_db.pkl --stringent
# False positives
python mirdeepsquared/extract_features.py resources/false_positives/result_08_11_2023_t_19_35_00.csv resources/false_positives/08_11_2023_t_19_35_00_output.mrd resources/dataset/false_positives_SRR2496781-84_bigger.pkl -fp --section novel
# Mouse
python mirdeepsquared/extract_features.py /Volumes/Mac/Users/jonatanjoensson/school/molecular-biology/mirdeep2-data/mouse/result_20_11_2023_t_14_26_34.csv /Volumes/Mac/Users/jonatanjoensson/school/molecular-biology/mirdeep2-data/mouse/output.mrd resources/dataset/other_species/true_positives/mouse/mouse.mature.pkl -tp --section known
python mirdeepsquared/mirgene_db_filter.py resources/dataset/other_species/true_positives/mouse/mouse.mature.pkl resources/ALL-precursors_in_mirgene_db.fas resources/dataset/other_species/true_positives/mouse/mouse.mature_only_mirgene_db.pkl -s
# Zebrafish
python mirdeepsquared/extract_features.py /Volumes/Mac/Users/jonatanjoensson/school/molecular-biology/mirdeep2-data/zebrafish/result_20_11_2023_t_14_11_15.csv /Volumes/Mac/Users/jonatanjoensson/school/molecular-biology/mirdeep2-data/zebrafish/output.mrd resources/dataset/other_species/zebrafish.mature.2nd.run.pkl -tp --section known
python mirdeepsquared/mirgene_db_filter.py resources/dataset/other_species/true_positives/zebrafish/zebrafish.mature.2nd.run.pkl resources/ALL-precursors_in_mirgene_db.fas resources/dataset/other_species/true_positives/zebrafish/zebrafish.mature.2nd.run_only_in_mirgene_db.pkl -s
# Zebrafish false positives
python mirdeepsquared/extract_features.py /Volumes/Mac/Users/jonatanjoensson/school/molecular-biology/mirdeep2-data/zebrafish/result_20_11_2023_t_14_11_15.csv /Volumes/Mac/Users/jonatanjoensson/school/molecular-biology/mirdeep2-data/zebrafish/output.mrd resources/dataset/other_species/possibly_false_positives/zebrafish.novel_b_default.pkl -fp --section novel
python mirdeepsquared/extract_features.py /Volumes/Mac/Users/jonatanjoensson/school/molecular-biology/mirdeep2-data/zebrafish/b-5/result_22_11_2023_t_14_45_02.csv /Volumes/Mac/Users/jonatanjoensson/school/molecular-biology/mirdeep2-data/zebrafish/b-5/output.mrd resources/dataset/other_species/zebrafish.novel_b_5.pkl -fp --section novel
python subset.py resources/dataset/other_species/zebrafish.novel_b_5.pkl resources/dataset/other_species/possibly_false_positives/zebrafish.novel_b_default.pkl resources/dataset/false_positives_zebrafish_b_less_than_zero.pkl
# Mouse false positives
python mirdeepsquared/extract_features.py /Volumes/Mac/Users/jonatanjoensson/school/molecular-biology/mirdeep2-data/mouse/result_20_11_2023_t_14_26_34.csv /Volumes/Mac/Users/jonatanjoensson/school/molecular-biology/mirdeep2-data/mouse/output.mrd resources/dataset/other_species/mouse.novel_b_default.pkl -fp --section novel
python mirdeepsquared/extract_features.py /Volumes/Mac/Users/jonatanjoensson/school/molecular-biology/mirdeep2-data/mouse/b-5/result_22_11_2023_t_14_28_31.csv /Volumes/Mac/Users/jonatanjoensson/school/molecular-biology/mirdeep2-data/mouse/b-5/output.mrd resources/dataset/other_species/mouse.novel_b_5.pkl -fp --section novel
python subset.py resources/dataset/other_species/mouse.novel_b_5.pkl resources/dataset/other_species/mouse.novel_b_default.pkl resources/dataset/false_positives_mouse_b_less_than_zero.pkl
python mirdeepsquared/correct_invalid_labels.py