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MakefileFigures
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# performance Savitski vs MaxQuant on Wang_base
Figure3a:
for database in swissprot_human_no_isoforms swissprot_human_with_isoforms uniprot_human; do \
mkdir -p $(DATA_DIR)/Wang_base/Wang_base_$${database}; \
python3 -um picked_group_fdr \
--mq_evidence $(DATA_DIR)/Wang_base/Wang_base_maxquant/evidence.txt \
--perc_evidence $(DATA_DIR)/Wang_base/Wang_base_percolator/peptides.all.txt \
--fasta $(DATA_DIR)/fasta/$${database}_prdb.fasta \
--suppress_missing_peptide_warning \
--protein_groups_out $(DATA_DIR)/Wang_base/Wang_base_$${database}/proteinGroups_$${database}.txt \
--methods savitski,maxquant \
| tee $(DATA_DIR)/manuscript_figures/Figure3a_$${database}.log; \
done
# calibration of Razor/Discard + Picked group
Figure4b:
mkdir -p $(DATA_DIR)/Wang_trap_0.5/Wang_trap_0.5_calibration_evaluation; \
python3 -um picked_group_fdr \
--mq_evidence $(DATA_DIR)/Wang_trap_0.5/Wang_trap_0.5_maxquant/evidence.txt \
--perc_evidence $(DATA_DIR)/Wang_trap_0.5/Wang_trap_0.5_percolator/peptides.all.txt \
--fasta $(DATA_DIR)/fasta/uniprot-proteome_human_190327.with_mimic_s0.5_m4.fasta \
--enzyme trypsinp \
--cleavages 0 \
--protein_groups_out $(DATA_DIR)/Wang_trap_0.5/Wang_trap_0.5_calibration_evaluation/proteinGroups.txt \
--figure_base_fn $(DATA_DIR)/manuscript_figures/Figure4b \
--methods discard_picked,razor_picked \
| tee $(DATA_DIR)/manuscript_figures/Figure4b.log;
# number of identified peptides unique and shared
Figure5b:
for database in swissprot_human_no_isoforms swissprot_human_with_isoforms uniprot_human; do \
python3 -um picked_group_fdr \
--perc_evidence $(DATA_DIR)/Wang_base/Wang_base_percolator/peptides.all.txt \
--fasta $(DATA_DIR)/fasta/$${database}_prdb.fasta \
--suppress_missing_peptide_warning \
--methods classic_no_grouping,classic_subset_grouping,classic_rescued_subset_grouping \
| tee $(DATA_DIR)/manuscript_figures/Figure5b_$${database}.log; \
done
# calibration of MaxQuant, Savitski, Classic protein group and Picked protein group
Figure5c:
mkdir -p $(DATA_DIR)/Wang_trap_0.5/Wang_trap_0.5_calibration_evaluation; \
python3 -um picked_group_fdr \
--mq_evidence $(DATA_DIR)/Wang_trap_0.5/Wang_trap_0.5_maxquant/evidence.txt \
--perc_evidence $(DATA_DIR)/Wang_trap_0.5/Wang_trap_0.5_percolator/peptides.all.txt \
--fasta $(DATA_DIR)/fasta/uniprot-proteome_human_190327.with_mimic_s0.5_m4.fasta \
--enzyme trypsinp \
--cleavages 0 \
--protein_groups_out $(DATA_DIR)/Wang_trap_0.5/Wang_trap_0.5_calibration_evaluation/proteinGroups.txt \
--figure_base_fn $(DATA_DIR)/manuscript_figures/Figure5c \
--methods maxquant,savitski,classic_protein_group,picked_protein_group \
| tee $(DATA_DIR)/manuscript_figures/Figure5c.log;
# performance MaxQuant, Savitski, Classic protein group and Picked protein group
Figure5d:
for database in swissprot_human_no_isoforms swissprot_human_with_isoforms uniprot_human; do \
mkdir -p $(DATA_DIR)/Wang_base/Wang_base_$${database}; \
python3 -um picked_group_fdr \
--mq_evidence $(DATA_DIR)/Wang_base/Wang_base_maxquant/evidence.txt \
--perc_evidence $(DATA_DIR)/Wang_base/Wang_base_percolator/peptides.all.txt \
--fasta $(DATA_DIR)/fasta/$${database}_prdb.fasta \
--suppress_missing_peptide_warning \
--protein_groups_out $(DATA_DIR)/Wang_base/Wang_base_$${database}/proteinGroups_$${database}.txt \
--methods maxquant,savitski,classic_protein_group,picked_protein_group \
| tee $(DATA_DIR)/manuscript_figures/Figure5d_$${database}.log; \
done
# Simulated data calibration and performance
Figure6:
for NUMEXP in 10 100 200 300 400 500; do \
python3 -um picked_group_fdr \
--mq_evidence $(DATA_DIR)/simulation/simulation_main_figure/evidence.$${NUMEXP}_experiments_peptFDR0.01_no_recalibration.txt \
--peptide_protein_map $(DATA_DIR)/fasta/uniprot-proteome_human_190327.peptide_to_protein_map.long_protein_ids.txt \
--mq_protein_groups $(DATA_DIR)/simulation/simulation_main_figure/proteinGroups.$${NUMEXP}_experiments_peptFDR0.01_no_recalibration.txt \
--protein_groups_out $(DATA_DIR)/simulation/simulation_main_figure_results/proteinGroups.$${NUMEXP}_experiments_peptFDR0.01_no_recalibration.txt \
--figure_base_fn $(DATA_DIR)/manuscript_figures/Figure6-$${NUMEXP}-experiments \
--methods maxquant,discard_picked_mq_input,razor_picked_mq_input,picked_protein_group_mq_input \
| tee $(DATA_DIR)/manuscript_figures/Figure6-$${NUMEXP}-experiments.log; \
done
# ProteomicsDB protein groups
Figure7a:
for database in swissprot_human_no_isoforms swissprot_human_with_isoforms uniprot_human; do \
python3 -um picked_group_fdr \
--perc_evidence $(DATA_DIR)/ProteomicsDB/ProteomicsDB_percolator_combined/percolator.$${database}.all.peptides.txt \
--protein_groups_out $(DATA_DIR)/ProteomicsDB/ProteomicsDB_picked_group_fdr/proteinGroups_$${database}.txt \
--fasta $(DATA_DIR)/fasta/$${database}_prdb.fasta \
--suppress_missing_peptide_warning \
--methods savitski_no_remap,picked_protein_group_no_remap \
| tee $(DATA_DIR)/manuscript_figures/Figure7a_$${database}.log; \
done
# MQ PEP is not well calibrated
SuppFigure1d:
python3 -um picked_group_fdr \
--mq_evidence $(DATA_DIR)/Wang_trap_0.5/Wang_trap_0.5_maxquant/evidence.txt \
--perc_evidence $(DATA_DIR)/Wang_trap_0.5/Wang_trap_0.5_percolator/peptides.all.txt \
--fasta $(DATA_DIR)/fasta/uniprot-proteome_human_190327.with_mimic_s0.5_m4.fasta \
--enzyme trypsinp \
--cleavages 0 \
--protein_groups_out $(DATA_DIR)/Wang_trap_0.5/Wang_trap_0.5_calibration_evaluation/proteinGroups.txt \
--figure_base_fn $(DATA_DIR)/manuscript_figures/Supplementary_Figure1d \
--methods savitski_mq_best,savitski_mq_mult,savitski,maxquant \
| tee $(DATA_DIR)/manuscript_figures/Supplementary_Figure1d.log
# performance all methods
SuppFigure2:
for fdr in "" _fdr0.1; do \
for database in swissprot_human_no_isoforms swissprot_human_with_isoforms uniprot_human; do \
mkdir -p $(DATA_DIR)/Wang_base/Wang_base_$${database}$${fdr}; \
python3 -um picked_group_fdr \
--mq_evidence $(DATA_DIR)/Wang_base/Wang_base_maxquant$${fdr}/evidence.txt \
--perc_evidence $(DATA_DIR)/Wang_base/Wang_base_percolator$${fdr}/peptides.all.txt \
--fasta $(DATA_DIR)/fasta/$${database}_prdb.fasta \
--suppress_missing_peptide_warning \
--protein_groups_out $(DATA_DIR)/Wang_base/Wang_base_$${database}$${fdr}/proteinGroups_$${database}.txt \
--methods maxquant,savitski_classic,savitski,discard_picked,razor_picked,classic_protein_group,picked_protein_group \
| tee $(DATA_DIR)/manuscript_figures/Supplementary_Figure2_$${database}$${fdr}.log; \
done; \
done
# number of unique and shared peptides in Wang_base
SuppFigure3:
for database in swissprot_human_no_isoforms swissprot_human_with_isoforms uniprot_human; do \
python3 -um picked_group_fdr \
--mq_evidence $(DATA_DIR)/Wang_base/Wang_base_maxquant/evidence.txt \
--perc_evidence $(DATA_DIR)/Wang_base/Wang_base_percolator/peptides.all.txt \
--fasta $(DATA_DIR)/fasta/$${database}_prdb.fasta \
--methods savitski \
--suppress_missing_peptide_warning \
| tee $(DATA_DIR)/manuscript_figures/Supplementary_Figure3_$${database}.log; \
done
# none of the razor approaches work
SuppFigure4:
python3 -um picked_group_fdr \
--mq_evidence $(DATA_DIR)/Wang_trap_0.5/Wang_trap_0.5_maxquant/evidence.txt \
--perc_evidence $(DATA_DIR)/Wang_trap_0.5/Wang_trap_0.5_percolator/peptides.all.txt \
--fasta $(DATA_DIR)/fasta/uniprot-proteome_human_190327.with_mimic_s0.5_m4.fasta \
--enzyme trypsinp \
--cleavages 0 \
--protein_groups_out $(DATA_DIR)/Wang_trap_0.5/Wang_trap_0.5_calibration_evaluation/proteinGroups.txt \
--figure_base_fn $(DATA_DIR)/manuscript_figures/Supplementary_Figure4 \
--methods maxquant,maxquant_mq_best,maxquant_perc_best,maxquant_picked,maxquant_mq_best_picked,maxquant_perc_best_picked \
| tee $(DATA_DIR)/manuscript_figures/Supplementary_Figure4.log
# calibration for all methods
SuppFigure5:
for ratio in 04 5; do \
mkdir -p $(DATA_DIR)/Wang_trap_0.$${ratio}/Wang_trap_0.$${ratio}_calibration_evaluation; \
python3 -um picked_group_fdr \
--mq_evidence $(DATA_DIR)/Wang_trap_0.$${ratio}/Wang_trap_0.$${ratio}_maxquant/evidence.txt \
--perc_evidence $(DATA_DIR)/Wang_trap_0.$${ratio}/Wang_trap_0.$${ratio}_percolator/peptides.all.txt \
--fasta $(DATA_DIR)/fasta/uniprot-proteome_human_190327.with_mimic_s0.$${ratio}_m4.fasta \
--enzyme trypsinp \
--cleavages 0 \
--figure_base_fn $(DATA_DIR)/manuscript_figures/Supplementary_Figure5_s0-$${ratio} \
--protein_groups_out $(DATA_DIR)/Wang_trap_0.$${ratio}/Wang_trap_0.$${ratio}_calibration_evaluation/proteinGroups.txt \
--methods maxquant,savitski_classic,savitski,discard_picked,razor_picked,classic_protein_group,picked_protein_group \
| tee $(DATA_DIR)/manuscript_figures/Supplementary_Figure5_s0.$${ratio}.log; \
done
# entrapment simulation verification - simulation
SuppFigure6a_d:
mkdir -p $(DATA_DIR)/simulation/simulation_supplementary_figures_results; \
for fdr in 1 01; do \
for ratio in 5 04; do \
python3 -um picked_group_fdr \
--mq_evidence $(DATA_DIR)/simulation/simulation_entrapment_analysis/evidence.mimic_s0.$${ratio}_m4_peptFDR0.$${fdr}.30_experiments.txt \
--peptide_protein_map $(DATA_DIR)/fasta/uniprot-proteome_human_190327.with_mimic_s0.$${ratio}_m4.peptide_to_protein_map.txt \
--mq_protein_groups $(DATA_DIR)/simulation/simulation_entrapment_analysis/proteinGroups.mimic_s0.$${ratio}_m4_peptFDR0.$${fdr}.30_experiments.txt \
--figure_base_fn $(DATA_DIR)/manuscript_figures/Supplementary_Figure6_simulation-s0-$${ratio}-fdr0-$${fdr} \
--protein_groups_out $(DATA_DIR)/simulation/simulation_supplementary_figures_results/proteinGroups_simulation-s0-$${ratio}-fdr0-$${fdr}.txt \
--methods maxquant,discard_picked_mq_input,razor_picked_mq_input,picked_protein_group_mq_input \
| tee $(DATA_DIR)/manuscript_figures/Supplementary_Figure6_simulation-s0-$${ratio}-fdr0-$${fdr}.log; \
done; \
done
# entrapment simulation verification - entrapment
SuppFigure6e_h:
for fdr in "" _fdr0.1; do \
for ratio in 5 04; do \
mkdir -p $(DATA_DIR)/Wang_trap_0.$${ratio}/Wang_trap_0.$${ratio}_calibration_evaluation$${fdr}; \
python3 -um picked_group_fdr \
--mq_evidence $(DATA_DIR)/Wang_trap_0.$${ratio}/Wang_trap_0.$${ratio}_maxquant$${fdr}/evidence.txt \
--perc_evidence $(DATA_DIR)/Wang_trap_0.$${ratio}/Wang_trap_0.$${ratio}_percolator$${fdr}/peptides.all.txt \
--fasta $(DATA_DIR)/fasta/uniprot-proteome_human_190327.with_mimic_s0.$${ratio}_m4.fasta \
--enzyme trypsinp \
--cleavages 0 \
--figure_base_fn $(DATA_DIR)/manuscript_figures/Supplementary_Figure6_entrapment-s0-$${ratio}$${fdr} \
--protein_groups_out $(DATA_DIR)/Wang_trap_0.$${ratio}/Wang_trap_0.$${ratio}_calibration_evaluation$${fdr}/proteinGroups.txt \
--methods maxquant,discard_picked,razor_picked,picked_protein_group \
| tee $(DATA_DIR)/manuscript_figures/Supplementary_Figure6_entrapment-s0-$${ratio}$${fdr}.log; \
done; \
done
# Simulated data calibration and performance 1% per experiment FDR
SuppFigure7:
mkdir -p $(DATA_DIR)/simulation/simulation_supplementary_figures_results; \
for NUMEXP in 100 200 500; do \
python3 -um picked_group_fdr \
--mq_evidence $(DATA_DIR)/simulation/simulation_supplementary_figures/evidence.$${NUMEXP}_experiments_peptFDR0.01_no_recalibration.txt \
--peptide_protein_map $(DATA_DIR)/fasta/uniprot-proteome_human_190327.peptide_to_protein_map.long_protein_ids.txt \
--mq_protein_groups $(DATA_DIR)/simulation/simulation_supplementary_figures/proteinGroups.$${NUMEXP}_experiments_peptFDR0.01_no_recalibration.txt \
--protein_groups_out $(DATA_DIR)/simulation/simulation_supplementary_figures_results/proteinGroups.$${NUMEXP}_experiments_peptFDR0.01_no_recalibration.txt \
--figure_base_fn $(DATA_DIR)/manuscript_figures/SuppFigure7-$${NUMEXP}-experiments \
--methods maxquant,discard_picked_mq_input,razor_picked_mq_input,picked_protein_group_mq_input \
| tee $(DATA_DIR)/manuscript_figures/SuppFigure7-$${NUMEXP}-experiments.log; \
done
# Simulated data calibration and performance 10% per experiment FDR
SuppFigure8:
mkdir -p $(DATA_DIR)/simulation/simulation_supplementary_figures_results; \
for NUMEXP in 100 200 500; do \
python3 -um picked_group_fdr \
--mq_evidence $(DATA_DIR)/simulation/simulation_supplementary_figures/evidence.$${NUMEXP}_experiments_peptFDR0.1_no_recalibration.txt \
--peptide_protein_map $(DATA_DIR)/fasta/uniprot-proteome_human_190327.peptide_to_protein_map.long_protein_ids.txt \
--mq_protein_groups $(DATA_DIR)/simulation/simulation_supplementary_figures/proteinGroups.$${NUMEXP}_experiments_peptFDR0.1_no_recalibration.txt \
--protein_groups_out $(DATA_DIR)/simulation/simulation_supplementary_figures_results/proteinGroups.$${NUMEXP}_experiments_peptFDR0.1_no_recalibration.txt \
--figure_base_fn $(DATA_DIR)/manuscript_figures/SuppFigure8-$${NUMEXP}-experiments \
--methods maxquant,discard_picked_mq_input,razor_picked_mq_input,picked_protein_group_mq_input \
| tee $(DATA_DIR)/manuscript_figures/SuppFigure8-$${NUMEXP}-experiments.log; \
done
# Simulated data calibration and performance 1% per experiment FDR
SuppFigure9:
mkdir -p $(DATA_DIR)/simulation/simulation_supplementary_figures_results; \
for NUMEXP in 100 200 500; do \
python3 -um picked_group_fdr \
--mq_evidence $(DATA_DIR)/simulation/simulation_supplementary_figures/evidence.$${NUMEXP}_experiments_peptFDR0.01_with_recalibration.txt \
--peptide_protein_map $(DATA_DIR)/fasta/uniprot-proteome_human_190327.peptide_to_protein_map.long_protein_ids.txt \
--mq_protein_groups $(DATA_DIR)/simulation/simulation_supplementary_figures/proteinGroups.$${NUMEXP}_experiments_peptFDR0.01_with_recalibration.txt \
--protein_groups_out $(DATA_DIR)/simulation/simulation_supplementary_figures_results/proteinGroups.$${NUMEXP}_experiments_peptFDR0.01_with_recalibration.txt \
--figure_base_fn $(DATA_DIR)/manuscript_figures/SuppFigure9-$${NUMEXP}-experiments \
--methods maxquant,discard_picked_mq_input,razor_picked_mq_input,picked_protein_group_mq_input \
| tee $(DATA_DIR)/manuscript_figures/SuppFigure9-$${NUMEXP}-experiments.log; \
done
# table with genes with multiple isoforms in SwissProt+isoforms
SuppTable2:
python3 -u picked_group_fdr/utils/get_genes_with_multiple_isoforms.py \
$(DATA_DIR)/ProteomicsDB/ProteomicsDB_picked_group_fdr/proteinGroups_swissprot_human_with_isoforms_picked_protein_group_fdr.txt \
$(DATA_DIR)/fasta/swissprot_human_with_isoforms_prdb.fasta \
$(DATA_DIR)/manuscript_figures/Supplementary_Table2.txt