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makefile
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### Top level installation variable definitions
parent_dir = $(shell pwd)
top_dir = $(parent_dir)
lib_dir_name = iXnos
lib_dir = $(top_dir)/$(lib_dir_name)
lib_files = \
$(lib_dir)/interface.py \
$(lib_dir)/lasagnenn.py \
$(lib_dir)/linreg.py \
$(lib_dir)/optimizecodons.py \
$(lib_dir)/plot.py \
$(lib_dir)/process.py \
$(lib_dir)/featureanalysis.py
genome_dir_name = genome_data
genome_dir = $(top_dir)/$(genome_dir_name)
yeast_gene_len_file = $(genome_dir)/scer.transcripts.13cds10.lengths.txt
yeast_gene_seq_file = $(genome_dir)/scer.transcripts.13cds10.fa
yeast_paralogs_file = $(genome_dir)/scer_100_80.paralogs.id.txt
yeast_gene_symbol_file = $(genome_dir)/scer_id_symbol.txt
yeast_codon_props_file = $(genome_dir)/yeast_codon_properties.txt
yeast_codon_anticodon_file = $(genome_dir)/yeast_codon_anticodon.csv
human_gene_len_file = $(genome_dir)/gencode.v22.transcript.13cds10.lengths.txt
human_gene_seq_file = $(genome_dir)/gencode.v22.transcript.13cds10.fa
genome_files = \
$(yeast_gene_len_file) \
$(yeast_gene_seq_file) \
$(yeast_paralogs_file) \
$(yeast_gene_symbol_file) \
$(yeast_codon_props_file) \
$(human_gene_len_file) \
$(human_gene_seq_file)
struc_dir_name = structure_data
struc_dir = $(top_dir)/$(struc_dir_name)
yeast_30_windows_seqs_file_zip = $(struc_dir)/scer.13cds10.windows.30len.fa.gz
yeast_30_windows_str_scores_file_zip = $(struc_dir)/scer.13cds10.windows.30len.fold.gz
yeast_30_windows_seqs_file = $(struc_dir)/scer.13cds10.windows.30len.fa
yeast_30_windows_str_scores_file = $(struc_dir)/scer.13cds10.windows.30len.fold
struc_files = \
$(yeast_30_windows_seqs_file) \
$(yeast_30_windows_str_scores_file)
wetlab_dir_name = wetlab_data
wetlab_dir = $(top_dir)/$(wetlab_dir_name)
circligase_qpcr_file = $(wetlab_dir)/circligase_qpcr.csv
mrna_data_file1 = $(wetlab_dir)/mrna_cy0_summary_20170906.csv
mrna_data_file2 = $(wetlab_dir)/mrna_cy0_summary_20171019.csv
mrna_data_file3 = $(wetlab_dir)/mrna_cy0_summary_20171030.csv
facs_data_zip_file = $(wetlab_dir)/gated-facs-data-20170829.csv.gz
facs_data_file = $(wetlab_dir)/gated-facs-data-20170829.csv
wetlab_files = \
$(circligase_qpcr_file) \
$(mrna_data_file1) \
$(mrna_data_file2) \
$(mrna_data_file3) \
$(facs_data_zip_file) \
$(facs_data_file)
comparison_dir_name = comparison_data
comparison_dir = $(top_dir)/$(comparison_dir_name)
oconnor_dir = $(comparison_dir)/OConnor
liu_dir = $(comparison_dir)/Liu
riboshape_dir = $(liu_dir)/riboshape
ASK_dir = $(riboshape_dir)/density_prediction/ASK_sigma[1,3,5,12.5,25,37.5,50,75]
repro_dir_name = reproduce_scripts
repro_dir = $(top_dir)/$(repro_dir_name)
repro_files = \
$(repro_dir)/process_data.py \
$(repro_dir)/feat_neighborhood_nn_series.py \
$(repro_dir)/feat_neighborhood_linreg_series.py \
$(repro_dir)/leaveout_series.py \
$(repro_dir)/struc_series.py \
$(repro_dir)/28mer_models.py \
$(repro_dir)/codon_scores.py \
$(repro_dir)/aggregate_mses.py \
$(repro_dir)/aggregate_linreg_mses.py \
$(repro_dir)/gene_corrs_by_density.py \
$(repro_dir)/plot_nn.py \
$(repro_dir)/plot_genes.py \
$(repro_dir)/paper_data.py \
$(repro_dir)/optimize_cds.py \
$(repro_dir)/pkl2txt.py \
$(repro_dir)/figure_1B_scaledcts.R \
$(repro_dir)/figure_1C_corrs.R \
$(repro_dir)/figure_1D_scatter.R \
$(repro_dir)/figure_1D_scatter_inset.R \
$(repro_dir)/figure_1E_indiv_gene.R \
$(repro_dir)/figure_1F_binned_error.R \
$(repro_dir)/figure_2A_downsampling.R \
$(repro_dir)/figure_2B_comparison.R \
$(repro_dir)/figure_3A_codoncorrs.R \
$(repro_dir)/figure_3B_heatmap.R \
$(repro_dir)/figure_3C_tai.R \
$(repro_dir)/figure_3C_wobble.R \
$(repro_dir)/figure_3D_lareaucodoncorrs.R \
$(repro_dir)/figure_3E_5prime.R \
$(repro_dir)/figure_3F_asite.R \
$(repro_dir)/figure_3G_cl2.R \
$(repro_dir)/figure_4B_citrine_dist.R \
$(repro_dir)/figure_4C_facs.R \
$(repro_dir)/figure_4D_te.R \
$(repro_dir)/supp_table_codon_scores.py \
$(repro_dir)/supp_figure_facs.R \
$(repro_dir)/supp_figure_mrna_qpcr.R \
$(repro_dir)/supp_figure_greencorrs.R \
$(repro_dir)/supp_figure_iwasakicorrs.R \
$(repro_dir)/supp_figure_cl1.R \
$(repro_dir)/supp_figure_cl1v2.R \
$(repro_dir)/supp_figure_liu_subspace.R \
$(repro_dir)/supp_figure_a_site.R \
$(repro_dir)/supp_figure_contexts.R
# $(repro_dir)/figure_1C_mse.R
# $(repro_dir)/figure_3A_codonmse.R
# $(repro_dir)/figure_3E_lareaucodonmse.R
# $(repro_dir)/supp_figure_greenmse.R
# $(repro_dir)/supp_figure_iwasakimse.R
expts_dir_name = expts
expts_dir = $(top_dir)/$(expts_dir_name)
expt_subdirs = process plots lasagne_nn linreg
results_dir_name = results
results_dir = $(top_dir)/$(results_dir_name)
fig_dir = $(results_dir)/figures
citrine_aa_seq = MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLGYGLMCFARYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSYQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK
### General experiment variable definitions
fp_sizes = $(shell seq -s ' ' 13 36)
10_epochs = $(shell seq -s ' ' 0 10)
15_epochs = $(shell seq -s ' ' 0 15)
20_epochs = $(shell seq -s ' ' 0 20)
25_epochs = $(shell seq -s ' ' 0 25)
30_epochs = $(shell seq -s ' ' 0 30)
35_epochs = $(shell seq -s ' ' 0 35)
40_epochs = $(shell seq -s ' ' 0 40)
45_epochs = $(shell seq -s ' ' 0 45)
50_epochs = $(shell seq -s ' ' 0 50)
55_epochs = $(shell seq -s ' ' 0 55)
60_epochs = $(shell seq -s ' ' 0 60)
65_epochs = $(shell seq -s ' ' 0 65)
70_epochs = $(shell seq -s ' ' 0 70)
75_epochs = $(shell seq -s ' ' 0 75)
nn_init_data_file_names = init_data.pkl y_te.pkl y_tr.pkl
nn_init_data_files = $(addprefix init_data/,$(nn_init_data_file_names))
nn_epoch_file_names = te_cost_by_epoch.pkl tr_cost_by_epoch.pkl weights.pkl \
y_te_hat.pkl y_tr_hat.pkl
nn_75_epoch_files = \
$(nn_init_data_files) \
$(foreach num,$(75_epochs),\
$(addprefix epoch$(num)/,$(nn_epoch_file_names)))
nn_70_epoch_files = \
$(nn_init_data_files) \
$(foreach num,$(70_epochs),\
$(addprefix epoch$(num)/,$(nn_epoch_file_names)))
nn_65_epoch_files = \
$(nn_init_data_files) \
$(foreach num,$(65_epochs),\
$(addprefix epoch$(num)/,$(nn_epoch_file_names)))
nn_60_epoch_files = \
$(nn_init_data_files) \
$(foreach num,$(60_epochs),\
$(addprefix epoch$(num)/,$(nn_epoch_file_names)))
nn_55_epoch_files = \
$(nn_init_data_files) \
$(foreach num,$(55_epochs),\
$(addprefix epoch$(num)/,$(nn_epoch_file_names)))
nn_50_epoch_files = \
$(nn_init_data_files) \
$(foreach num,$(50_epochs),\
$(addprefix epoch$(num)/,$(nn_epoch_file_names)))
nn_45_epoch_files = \
$(nn_init_data_files) \
$(foreach num,$(45_epochs),\
$(addprefix epoch$(num)/,$(nn_epoch_file_names)))
nn_40_epoch_files = \
$(nn_init_data_files) \
$(foreach num,$(40_epochs),\
$(addprefix epoch$(num)/,$(nn_epoch_file_names)))
nn_35_epoch_files = \
$(nn_init_data_files) \
$(foreach num,$(35_epochs),\
$(addprefix epoch$(num)/,$(nn_epoch_file_names)))
nn_30_epoch_files = \
$(nn_init_data_files) \
$(foreach num,$(30_epochs),\
$(addprefix epoch$(num)/,$(nn_epoch_file_names)))
nn_25_epoch_files = \
$(nn_init_data_files) \
$(foreach num,$(25_epochs),\
$(addprefix epoch$(num)/,$(nn_epoch_file_names)))
nn_20_epoch_files = \
$(nn_init_data_files) \
$(foreach num,$(20_epochs),\
$(addprefix epoch$(num)/,$(nn_epoch_file_names)))
nn_15_epoch_files = \
$(nn_init_data_files) \
$(foreach num,$(15_epochs),\
$(addprefix epoch$(num)/,$(nn_epoch_file_names)))
nn_10_epoch_files = \
$(nn_init_data_files) \
$(foreach num,$(10_epochs),\
$(addprefix epoch$(num)/,$(nn_epoch_file_names)))
plot_files = cts_by_size.pdf \
${addprefix size_,${addsuffix _by_frame.pdf,${fp_sizes}}}
plot_files_pattern = cts_by_size%pdf \
${addprefix size_,${addsuffix _by_frame%pdf,${fp_sizes}}}
10_reps = $(shell seq -s ' ' 0 9)
feat_neighborhoods = \
cod_p0 cod_p0_nt_p0p2 cod_n3p2 cod_n3p2_nt_n9p8 \
cod_n5p4 cod_n5p4_nt_n15p14 cod_n7p5 cod_n7p5_nt_n21p17
leaveout_cods = $(shell seq -s ' ' -7 5)
linreg_data_files = \
linreg_data.txt wts.pkl \
y_te.pkl y_te_hat.pkl \
y_tr.pkl y_tr_hat.pkl
linreg_plot_files = \
tr_scatter.pdf te_scatter.pdf \
tr_bin_err.pdf te_bin_err.pdf \
tr_cum_err.pdf te_cum_err.pdf
nn_plot_files = \
tr_cost_by_epoch.pdf te_cost_by_epoch.pdf \
tr_scatter.pdf te_scatter.pdf \
tr_bin_err.pdf te_bin_err.pdf \
tr_cum_err.pdf te_cum_err.pdf
### Weinberg variable definitions
weinberg_expt_dir_name = weinberg
weinberg_expt_dir = $(expts_dir)/$(weinberg_expt_dir_name)
weinberg_proc_dir = $(weinberg_expt_dir)/process
weinberg_plot_dir = $(weinberg_expt_dir)/plots
weinberg_nn_dir = $(weinberg_expt_dir)/lasagne_nn
weinberg_lr_dir = $(weinberg_expt_dir)/linreg
weinberg_subdirs = $(addprefix $(weinberg_expt_dir)/,$(expt_subdirs))
weinberg_subdirs_pattern = $(addprefix $(weinberg_expt_dir)%,$(expt_subdirs))
weinberg_gene_len_file = $(genome_dir)/yeast_13cds10_lengths.txt
weinberg_gene_seq_file = $(genome_dir)/yeast_13cds10.fa
weinberg_raw_fastq_file = $(weinberg_proc_dir)/SRR1049521.fastq
weinberg_trimmer_script = $(weinberg_proc_dir)/trim_linker_weinberg.pl
weinberg_mapping_script = $(weinberg_proc_dir)/weinberg.sh
weinberg_raw_sam_file = $(weinberg_expt_dir)/process/weinberg.transcript.sam
weinberg_mapped_sam_file = $(weinberg_expt_dir)/process/weinberg.transcript.mapped.sam
weinberg_sam_file = $(weinberg_expt_dir)/process/weinberg.transcript.mapped.wts.sam
weinberg_plot_files = ${addprefix ${weinberg_plot_dir}/,${plot_files}}
weinberg_plot_files_pattern = \
${addprefix ${weinberg_plot_dir}/,${plot_files_pattern}}
weinberg_27_31_cts_by_codon = $(weinberg_proc_dir)/cts_by_codon.size.27.31.txt
weinberg_27_31_outputs = $(weinberg_proc_dir)/outputs.size.27.31.txt
weinberg_27_31_te_bounds = $(weinberg_proc_dir)/te_set_bounds.size.27.31.trunc.20.20.min_cts.200.min_cod.100.top.500.txt
weinberg_27_31_te_data_table = $(weinberg_proc_dir)/te_set_bounds.size.27.31.trunc.20.20.min_cts.200.min_cod.100.top.500.data_table.txt
weinberg_27_31_tr_bounds = $(weinberg_proc_dir)/tr_set_bounds.size.27.31.trunc.20.20.min_cts.200.min_cod.100.top.500.txt
weinberg_27_31_tr_data_table = $(weinberg_proc_dir)/tr_set_bounds.size.27.31.trunc.20.20.min_cts.200.min_cod.100.top.500.data_table.txt
weinberg_27_31_proc_sam_files = \
$(weinberg_27_31_cts_by_codon) \
$(weinberg_27_31_outputs) \
$(weinberg_27_31_te_bounds) \
$(weinberg_27_31_te_data_table) \
$(weinberg_27_31_tr_bounds) \
$(weinberg_27_31_tr_data_table)
weinberg_27_31_proc_sam_pattern = \
$(subst .txt,%txt,$(weinberg_27_31_cts_by_codon)) \
$(subst .txt,%txt,$(weinberg_27_31_outputs)) \
$(subst .txt,%txt,$(weinberg_27_31_te_bounds)) \
$(subst .txt,%txt,$(weinberg_27_31_te_data_table)) \
$(subst .txt,%txt,$(weinberg_27_31_tr_bounds)) \
$(subst .txt,%txt,$(weinberg_27_31_tr_data_table))
weinberg_28_cts_by_codon = $(weinberg_proc_dir)/cts_by_codon.size.28.28.txt
weinberg_28_outputs = $(weinberg_proc_dir)/outputs.size.28.28.txt
weinberg_28_te_bounds = $(weinberg_proc_dir)/te_set_bounds.size.28.28.trunc.20.20.min_cts.200.min_cod.100.top.500.txt
weinberg_28_te_data_table = $(weinberg_proc_dir)/te_set_bounds.size.28.28.trunc.20.20.min_cts.200.min_cod.100.top.500.data_table.txt
weinberg_28_tr_bounds = $(weinberg_proc_dir)/tr_set_bounds.size.28.28.trunc.20.20.min_cts.200.min_cod.100.top.500.txt
weinberg_28_tr_data_table = $(weinberg_proc_dir)/tr_set_bounds.size.28.28.trunc.20.20.min_cts.200.min_cod.100.top.500.data_table.txt
weinberg_28_proc_sam_files = \
$(weinberg_28_cts_by_codon) \
$(weinberg_28_outputs) \
$(weinberg_28_te_bounds) \
$(weinberg_28_te_data_table) \
$(weinberg_28_tr_bounds) \
$(weinberg_28_tr_data_table)
weinberg_28_proc_sam_pattern = \
$(subst .txt,%txt,$(weinberg_28_cts_by_codon)) \
$(subst .txt,%txt,$(weinberg_28_outputs)) \
$(subst .txt,%txt,$(weinberg_28_te_bounds)) \
$(subst .txt,%txt,$(weinberg_28_te_data_table)) \
$(subst .txt,%txt,$(weinberg_28_tr_bounds)) \
$(subst .txt,%txt,$(weinberg_28_tr_data_table))
weinberg_feat_nb_series_files = $(foreach feat_nb,$(feat_neighborhoods),$(foreach rep,$(10_reps),$(addprefix $(weinberg_nn_dir)/full_$(feat_nb)_rep$(rep)/,$(nn_60_epoch_files))))
weinberg_feat_nb_series_pattern = $(addprefix $(weinberg_nn_dir)/full_%/,$(nn_60_epoch_files))
weinberg_leaveout_series_files = $(foreach lo_cod,$(leaveout_cods),$(foreach rep,$(10_reps),$(addprefix $(weinberg_nn_dir)/nocod$(lo_cod)_cod_n7p5_nt_n21p17_rep$(rep)/,$(nn_60_epoch_files))))
weinberg_leaveout_series_pattern = $(addprefix $(weinberg_nn_dir)/nocod%/,$(nn_60_epoch_files))
weinberg_28_files = $(addprefix $(weinberg_nn_dir)/s28_cod_n5p4_nt_n15p14/,$(nn_60_epoch_files))
weinberg_28_pattern = $(addprefix $(weinberg_nn_dir)/s28_%/,$(nn_60_epoch_files))
weinberg_fp_struc_files = $(foreach rep,$(10_reps),$(addprefix $(weinberg_nn_dir)/str_n17n15_cod_n5p4_nt_n15p14_rep$(rep)/,$(nn_55_epoch_files)))
weinberg_fp_struc_pattern = $(addprefix $(weinberg_nn_dir)/str_%/,$(nn_55_epoch_files))
weinberg_max_struc_files = $(foreach rep,$(10_reps),$(addprefix $(weinberg_nn_dir)/max_str_p13p42_cod_n5p4_nt_n15p14_rep$(rep)/,$(nn_70_epoch_files)))
weinberg_max_struc_pattern = $(addprefix $(weinberg_nn_dir)/max_str_%/,$(nn_70_epoch_files))
weinberg_noAsite_n3p2_series_files = $(addprefix $(weinberg_nn_dir)/noAsite_cod_n3p2_nt_n9p8/,$(nn_60_epoch_files))
weinberg_noAsite_n3p2_series_pattern = $(addprefix $(weinberg_nn_dir)/noAsite%/,$(nn_60_epoch_files))
weinberg_linreg_series_files = $(foreach feat_nb,$(feat_neighborhoods),$(addprefix $(weinberg_lr_dir)/lr_$(feat_nb)/,$(linreg_data_files)))
weinberg_linreg_series_pattern = $(addprefix $(weinberg_lr_dir)/lr_%/,$(linreg_data_files))
weinberg_struc_plot_files = $(addprefix $(weinberg_nn_dir)/str_n17n15_cod_n5p4_nt_n15p14_rep0/plots/,$(nn_plot_files))
weinberg_struc_plot_pattern = $(addprefix $(weinberg_nn_dir)/str_n17n15_cod_n5p4_nt_n15p14_rep0/plot%/,$(nn_plot_files))
weinberg_full_plot_files = $(addprefix $(weinberg_nn_dir)/full_cod_n5p4_nt_n15p14_rep0/plots/,$(nn_plot_files))
weinberg_full_plot_pattern = $(addprefix $(weinberg_nn_dir)/full_cod_n5p4_nt_n15p14_rep0/plot%/,$(nn_plot_files))
weinberg_28_plot_files = $(addprefix $(weinberg_nn_dir)/s28_cod_n5p4_nt_n15p14/plots/,$(nn_plot_files))
weinberg_28_plot_pattern = $(addprefix $(weinberg_nn_dir)/s28_cod_n5p4_nt_n15p14/plot%/,$(nn_plot_files))
weinberg_struc_gene_plot_dir = $(weinberg_nn_dir)/str_n17n15_cod_n5p4_nt_n15p14_rep0/gene_plots
weinberg_feat_nb_series_num_epochs = 60
weinberg_feat_nb_series_lr_decay = 16
weinberg_feat_nb_series_num_reps = 10
weinberg_leaveout_series_num_epochs = $(weinberg_feat_nb_series_num_epochs)
weinberg_leaveout_series_lr_decay = $(weinberg_feat_nb_series_lr_decay)
weinberg_leaveout_series_num_reps = $(weinberg_feat_nb_series_num_reps)
weinberg_28_num_epochs = 60
weinberg_28_lr_decay = 8
weinberg_28_num_reps = 10
weinberg_fp_struc_num_epochs = 55
weinberg_fp_struc_lr_decay = 16
weinberg_fp_struc_num_reps = 10
# Could be 65
weinberg_max_struc_num_epochs = 70
weinberg_max_struc_lr_decay = 32
weinberg_max_struc_num_reps = 10
# Weinberg results files variable definitions
weinberg_results_dir = $(results_dir)/weinberg
weinberg_results_feat_neighborhood_dir = \
$(weinberg_results_dir)/feat_neighborhood_series
weinberg_results_leaveout_dir = $(weinberg_results_dir)/leaveout_series
weinberg_results_struc_series_dir = $(weinberg_results_dir)/structure_series
weinberg_results_struc_dir = $(weinberg_results_dir)/str_n17n15_cod_n5p4_nt_n15p14_rep0
weinberg_results_struc_epoch_dir = $(weinberg_results_struc_dir)/epoch$(weinberg_fp_struc_num_epochs)
weinberg_results_full_dir = $(weinberg_results_dir)/full_cod_n5p4_nt_n15p14_rep0
weinberg_results_full_epoch_dir = $(weinberg_results_full_dir)/epoch$(weinberg_feat_nb_series_num_epochs)
weinberg_results_28_dir = $(weinberg_results_dir)/s28_cod_n5p4_nt_n15p14
weinberg_results_28_epoch_dir = $(weinberg_results_28_dir)/epoch$(weinberg_28_num_epochs)
weinberg_results_opt_model_dir = $(weinberg_results_dir)/full_cod_n3p2_nt_n9p8_rep0
weinberg_results_opt_model_epoch_dir = $(weinberg_results_opt_model_dir)/epoch$(weinberg_feat_nb_series_num_epochs)
#weinberg_results_n3p2_dir = $(weinberg_results_dir)/full_cod_n3p2_nt_n9p8_rep0
#weinberg_results_n3p2_epoch_dir = $(weinberg_results_n3p2_dir)/epoch$(weinberg_feat_nb_series_num_epochs)
weinberg_results_p0_dir = $(weinberg_results_dir)/full_cod_p0_nt_p0p2_rep0
weinberg_results_p0_epoch_dir = $(weinberg_results_p0_dir)/epoch$(weinberg_feat_nb_series_num_epochs)
weinberg_results_noAsite_n3p2_dir = $(weinberg_results_dir)/noAsite_cod_n3p2_nt_n9p8
weinberg_results_noAsite_n3p2_epoch_dir = $(weinberg_results_noAsite_n3p2_dir)/epoch$(weinberg_feat_nb_series_num_epochs)
weinberg_full_analysis_epoch_dir = $(weinberg_nn_dir)/full_cod_n5p4_nt_n15p14_rep0/epoch$(weinberg_feat_nb_series_num_epochs)
weinberg_28_analysis_epoch_dir = $(weinberg_nn_dir)/s28_cod_n5p4_nt_n15p14/epoch$(weinberg_28_num_epochs)
weinberg_full_codon_scores_results_files = \
$(weinberg_results_full_epoch_dir)/codon_scores.tsv \
$(weinberg_results_full_epoch_dir)/codon_scores_colormap.pdf
weinberg_full_codon_scores_results_files_pattern = \
$(weinberg_results_full_epoch_dir)/codon_scores%tsv \
$(weinberg_results_full_epoch_dir)/codon_scores_colormap%pdf
weinberg_28_codon_scores_results_files = \
$(weinberg_results_28_epoch_dir)/codon_scores.tsv \
$(weinberg_results_28_epoch_dir)/codon_scores_colormap.pdf
weinberg_28_codon_scores_results_files_pattern = \
$(weinberg_results_28_epoch_dir)/codon_scores%tsv \
$(weinberg_results_28_epoch_dir)/codon_scores_colormap%pdf
weinberg_feat_nb_mses_file = \
$(weinberg_results_feat_neighborhood_dir)/feat_neighborhood_mses.txt
weinberg_feat_nb_linreg_mses_file = \
$(weinberg_results_feat_neighborhood_dir)/linreg_mses.txt
weinberg_leaveout_mses_file = \
$(weinberg_results_leaveout_dir)/leaveout_mses.txt
weinberg_struc_mses_file = \
$(weinberg_results_struc_series_dir)/struc_mses.txt
weinberg_feat_nb_corrs_file = \
$(weinberg_results_feat_neighborhood_dir)/feat_neighborhood_corrs.txt
weinberg_feat_nb_linreg_corrs_file = \
$(weinberg_results_feat_neighborhood_dir)/linreg_corrs.txt
weinberg_leaveout_corrs_file = \
$(weinberg_results_leaveout_dir)/leaveout_corrs.txt
weinberg_struc_corrs_file = \
$(weinberg_results_struc_series_dir)/struc_corrs.txt
weinberg_struc_corrs_by_gene_density_file = \
$(weinberg_results_struc_epoch_dir)/corrs_by_gene_density.txt
weinberg_final_model_y_te = $(weinberg_nn_dir)/str_n17n15_cod_n5p4_nt_n15p14_rep0/init_data/y_te.txt
weinberg_final_model_y_te_hat = $(weinberg_nn_dir)/str_n17n15_cod_n5p4_nt_n15p14_rep0/epoch$(weinberg_fp_struc_num_epochs)/y_te_hat.txt \
weinberg_results_final_model_y_te = $(weinberg_results_struc_epoch_dir)/y_te.txt
weinberg_results_final_model_y_te_hat = $(weinberg_results_struc_epoch_dir)/y_te_hat.txt
weinberg_opt_series_file = $(weinberg_results_opt_model_epoch_dir)/citrine_opt_series.txt
weinberg_opt_model_epoch_dir = $(weinberg_nn_dir)/full_cod_n3p2_nt_n9p8_rep0/epoch$(weinberg_feat_nb_series_num_epochs)
weinberg_results_opt_model_y_te_hat = $(weinberg_results_opt_model_epoch_dir)/y_te_hat.txt
weinberg_p0_epoch_dir = $(weinberg_nn_dir)/full_cod_p0_nt_p0p2_rep0/epoch$(weinberg_feat_nb_series_num_epochs)
weinberg_results_p0_y_te_hat = $(weinberg_results_p0_epoch_dir)/y_te_hat.txt
weinberg_noAsite_n3p2_epoch_dir = $(weinberg_nn_dir)/noAsite_cod_n3p2_nt_n9p8/epoch$(weinberg_feat_nb_series_num_epochs)
weinberg_results_noAsite_n3p2_y_te_hat = $(weinberg_results_noAsite_n3p2_epoch_dir)/y_te_hat.txt
### Lareau variable definitions
lareau_expt_dir_name = lareau
lareau_expt_dir = $(expts_dir)/$(lareau_expt_dir_name)
lareau_proc_dir = $(lareau_expt_dir)/process
lareau_plot_dir = $(lareau_expt_dir)/plots
lareau_nn_dir = $(lareau_expt_dir)/lasagne_nn
lareau_lr_dir = $(lareau_expt_dir)/linreg
lareau_subdirs = $(addprefix $(lareau_expt_dir)/,$(expt_subdirs))
lareau_subdirs_pattern = $(addprefix $(lareau_expt_dir)%,$(expt_subdirs))
lareau_gene_len_file = $(genome_dir)/yeast_13cds10_lengths.txt
lareau_gene_seq_file = $(genome_dir)/yeast_13cds10.fa
lareau_raw_fastq_file_1 = $(lareau_proc_dir)/SRR6260802.fastq
lareau_raw_fastq_file_2 = $(lareau_proc_dir)/SRR6260803.fastq
lareau_raw_fastq_files = \
$(lareau_proc_dir)/SRR6260802.fastq \
$(lareau_proc_dir)/SRR6260803.fastq
lareau_trimmer_script = $(lareau_proc_dir)/trim_linker_bc.pl
lareau_mapping_script = $(lareau_proc_dir)/lareau.sh
lareau_raw_sam_file = $(lareau_expt_dir)/process/lareau.transcript.sam
lareau_mapped_sam_file = $(lareau_expt_dir)/process/lareau.transcript.mapped.sam
lareau_sam_file = $(lareau_expt_dir)/process/lareau.transcript.mapped.wts.sam
lareau_plot_files = ${addprefix ${lareau_plot_dir}/,${plot_files}}
lareau_plot_files_pattern = \
${addprefix ${lareau_plot_dir}/,${plot_files_pattern}}
lareau_27_29_cts_by_codon = $(lareau_proc_dir)/cts_by_codon.size.27.29.txt
lareau_27_29_outputs = $(lareau_proc_dir)/outputs.size.27.29.txt
lareau_27_29_te_bounds = $(lareau_proc_dir)/te_set_bounds.size.27.29.trunc.20.20.min_cts.200.min_cod.100.top.500.txt
lareau_27_29_te_data_table = $(lareau_proc_dir)/te_set_bounds.size.27.29.trunc.20.20.min_cts.200.min_cod.100.top.500.data_table.txt
lareau_27_29_tr_bounds = $(lareau_proc_dir)/tr_set_bounds.size.27.29.trunc.20.20.min_cts.200.min_cod.100.top.500.txt
lareau_27_29_tr_data_table = $(lareau_proc_dir)/tr_set_bounds.size.27.29.trunc.20.20.min_cts.200.min_cod.100.top.500.data_table.txt
lareau_27_29_proc_sam_files = \
$(lareau_27_29_cts_by_codon) \
$(lareau_27_29_outputs) \
$(lareau_27_29_te_bounds) \
$(lareau_27_29_te_data_table) \
$(lareau_27_29_tr_bounds) \
$(lareau_27_29_tr_data_table)
lareau_27_29_proc_sam_pattern = \
$(subst .txt,%txt,$(lareau_27_29_cts_by_codon)) \
$(subst .txt,%txt,$(lareau_27_29_outputs)) \
$(subst .txt,%txt,$(lareau_27_29_te_bounds)) \
$(subst .txt,%txt,$(lareau_27_29_te_data_table)) \
$(subst .txt,%txt,$(lareau_27_29_tr_bounds)) \
$(subst .txt,%txt,$(lareau_27_29_tr_data_table))
lareau_28_cts_by_codon = $(lareau_proc_dir)/cts_by_codon.size.28.28.txt
lareau_28_outputs = $(lareau_proc_dir)/outputs.size.28.28.txt
lareau_28_te_bounds = $(lareau_proc_dir)/te_set_bounds.size.28.28.trunc.20.20.min_cts.200.min_cod.100.top.500.txt
lareau_28_te_data_table = $(lareau_proc_dir)/te_set_bounds.size.28.28.trunc.20.20.min_cts.200.min_cod.100.top.500.data_table.txt
lareau_28_tr_bounds = $(lareau_proc_dir)/tr_set_bounds.size.28.28.trunc.20.20.min_cts.200.min_cod.100.top.500.txt
lareau_28_tr_data_table = $(lareau_proc_dir)/tr_set_bounds.size.28.28.trunc.20.20.min_cts.200.min_cod.100.top.500.data_table.txt
lareau_28_proc_sam_files = \
$(lareau_28_cts_by_codon) \
$(lareau_28_outputs) \
$(lareau_28_te_bounds) \
$(lareau_28_te_data_table) \
$(lareau_28_tr_bounds) \
$(lareau_28_tr_data_table)
lareau_28_proc_sam_pattern = \
$(subst .txt,%txt,$(lareau_28_cts_by_codon)) \
$(subst .txt,%txt,$(lareau_28_outputs)) \
$(subst .txt,%txt,$(lareau_28_te_bounds)) \
$(subst .txt,%txt,$(lareau_28_te_data_table)) \
$(subst .txt,%txt,$(lareau_28_tr_bounds)) \
$(subst .txt,%txt,$(lareau_28_tr_data_table))
lareau_full_model_files = \
$(foreach rep,$(10_reps),$(addprefix \
$(lareau_nn_dir)/full_cod_n5p4_nt_n15p14_rep$(rep)/,\
$(nn_35_epoch_files)))
lareau_full_model_pattern = $(addprefix $(lareau_nn_dir)/full_%/,\
$(nn_35_epoch_files))
lareau_exp_model_files = \
$(foreach rep,$(10_reps),$(addprefix \
$(lareau_nn_dir)/full_cod_n7p5_nt_n21p17_rep$(rep)/,\
$(nn_35_epoch_files)))
lareau_exp_model_pattern = $(addprefix $(lareau_nn_dir)/full_%/,\
$(nn_35_epoch_files))
lareau_leaveout_series_files = \
$(foreach lo_cod,$(leaveout_cods),\
$(foreach rep,$(10_reps), $(addprefix \
$(lareau_nn_dir)/nocod$(lo_cod)_cod_n7p5_nt_n21p17_rep$(rep)/,\
$(nn_35_epoch_files))))
lareau_leaveout_series_pattern = $(addprefix $(lareau_nn_dir)/nocod%/,\
$(nn_35_epoch_files))
lareau_28_files = $(addprefix $(lareau_nn_dir)/s28_cod_n5p4_nt_n15p14/,\
$(nn_40_epoch_files))
lareau_28_pattern = $(addprefix $(lareau_nn_dir)/s28_%/,$(nn_40_epoch_files))
lareau_full_plot_files = $(addprefix $(lareau_nn_dir)/full_cod_n5p4_nt_n15p14_rep0/plots/,$(nn_plot_files))
lareau_full_plot_pattern = $(addprefix $(lareau_nn_dir)/full_cod_n5p4_nt_n15p14_rep0/plot%/,$(nn_plot_files))
lareau_28_plot_files = $(addprefix $(lareau_nn_dir)/s28_cod_n5p4_nt_n15p14/plots/,$(nn_plot_files))
lareau_28_plot_pattern = $(addprefix $(lareau_nn_dir)/s28_cod_n5p4_nt_n15p14/plot%/,$(nn_plot_files))
lareau_feat_nb_series_num_epochs = 35
lareau_feat_nb_series_lr_decay = 8
lareau_feat_nb_series_num_reps = 10
lareau_leaveout_series_num_epochs = $(lareau_feat_nb_series_num_epochs)
lareau_leaveout_series_lr_decay = $(lareau_feat_nb_series_lr_decay)
lareau_leaveout_series_num_reps = $(lareau_feat_nb_series_num_reps)
lareau_28_num_epochs = 40
lareau_28_lr_decay = 4
lareau_28_num_reps = 10
# Lareau results files variable definitions
lareau_results_dir = $(results_dir)/lareau
lareau_results_feat_neighborhood_dir = \
$(lareau_results_dir)/feat_neighborhood_series
lareau_results_leaveout_dir = $(lareau_results_dir)/leaveout_series
lareau_results_full_dir = $(lareau_results_dir)/full_cod_n5p4_nt_n15p14_rep0
lareau_results_full_epoch_dir = $(lareau_results_full_dir)/epoch$(lareau_feat_nb_series_num_epochs)
lareau_results_28_dir = $(lareau_results_dir)/s28_cod_n5p4_nt_n15p14
lareau_results_28_epoch_dir = $(lareau_results_28_dir)/epoch$(lareau_28_num_epochs)
lareau_full_analysis_epoch_dir = $(lareau_nn_dir)/full_cod_n5p4_nt_n15p14_rep0/epoch$(lareau_feat_nb_series_num_epochs)
lareau_28_analysis_epoch_dir = $(lareau_nn_dir)/s28_cod_n5p4_nt_n15p14/epoch$(lareau_28_num_epochs)
lareau_full_codon_scores_results_files = \
$(lareau_results_full_epoch_dir)/codon_scores.tsv \
$(lareau_results_full_epoch_dir)/codon_scores_colormap.pdf
lareau_full_codon_scores_results_files_pattern = \
$(lareau_results_full_epoch_dir)/codon_scores%tsv \
$(lareau_results_full_epoch_dir)/codon_scores_colormap%pdf
lareau_28_codon_scores_results_files = \
$(lareau_results_28_epoch_dir)/codon_scores.tsv \
$(lareau_results_28_epoch_dir)/codon_scores_colormap.pdf
lareau_28_codon_scores_results_files_pattern = \
$(lareau_results_28_epoch_dir)/codon_scores%tsv \
$(lareau_results_28_epoch_dir)/codon_scores_colormap%pdf
lareau_feat_nb_corrs_file = \
$(lareau_results_feat_neighborhood_dir)/feat_neighborhood_corrs.txt
lareau_leaveout_mses_file = \
$(lareau_results_leaveout_dir)/leaveout_mses.txt
lareau_leaveout_corrs_file = \
$(lareau_results_leaveout_dir)/leaveout_corrs.txt
### Iwasaki variable definitions
iwasaki_expt_dir_name = iwasaki
iwasaki_expt_dir = $(expts_dir)/$(iwasaki_expt_dir_name)
iwasaki_proc_dir = $(iwasaki_expt_dir)/process
iwasaki_plot_dir = $(iwasaki_expt_dir)/plots
iwasaki_nn_dir = $(iwasaki_expt_dir)/lasagne_nn
iwasaki_lr_dir = $(iwasaki_expt_dir)/linreg
iwasaki_subdirs = $(addprefix $(iwasaki_expt_dir)/,$(expt_subdirs))
iwasaki_subdirs_pattern = $(addprefix $(iwasaki_expt_dir)%,$(expt_subdirs))
iwasaki_gene_len_file = $(genome_dir)/gencode.v22.transcript.13cds10.lengths.txt
iwasaki_gene_seq_file = $(genome_dir)/gencode.v22.transcript.13cds10.fa
iwasaki_raw_fastq_files = \
$(iwasaki_proc_dir)/SRR2075925.fastq \
$(iwasaki_proc_dir)/SRR2075926.fastq
iwasaki_trimmer_script = $(iwasaki_proc_dir)/trim_linker.pl
iwasaki_mapping_script = $(iwasaki_proc_dir)/iwasaki.sh
iwasaki_raw_sam_file = $(iwasaki_expt_dir)/process/iwasaki.transcript.sam
iwasaki_mapped_sam_file = $(iwasaki_expt_dir)/process/iwasaki.transcript.mapped.sam
iwasaki_sam_file = $(iwasaki_expt_dir)/process/iwasaki.transcript.mapped.wts.sam
iwasaki_plot_files = ${addprefix ${iwasaki_plot_dir}/,${plot_files}}
iwasaki_plot_files_pattern = \
${addprefix ${iwasaki_plot_dir}/,${plot_files_pattern}}
iwasaki_27_30_cts_by_codon = $(iwasaki_proc_dir)/cts_by_codon.size.27.30.txt
iwasaki_27_30_outputs = $(iwasaki_proc_dir)/outputs.size.27.30.txt
iwasaki_27_30_te_bounds = $(iwasaki_proc_dir)/te_set_bounds.size.27.30.trunc.20.20.min_cts.200.min_cod.100.top.500.txt
iwasaki_27_30_te_data_table = $(iwasaki_proc_dir)/te_set_bounds.size.27.30.trunc.20.20.min_cts.200.min_cod.100.top.500.data_table.txt
iwasaki_27_30_tr_bounds = $(iwasaki_proc_dir)/tr_set_bounds.size.27.30.trunc.20.20.min_cts.200.min_cod.100.top.500.txt
iwasaki_27_30_tr_data_table = $(iwasaki_proc_dir)/tr_set_bounds.size.27.30.trunc.20.20.min_cts.200.min_cod.100.top.500.data_table.txt
iwasaki_27_30_proc_sam_files = \
$(iwasaki_27_30_cts_by_codon) \
$(iwasaki_27_30_outputs) \
$(iwasaki_27_30_te_bounds) \
$(iwasaki_27_30_te_data_table) \
$(iwasaki_27_30_tr_bounds) \
$(iwasaki_27_30_tr_data_table)
iwasaki_27_30_proc_sam_pattern = \
$(subst .txt,%txt,$(iwasaki_27_30_cts_by_codon)) \
$(subst .txt,%txt,$(iwasaki_27_30_outputs)) \
$(subst .txt,%txt,$(iwasaki_27_30_te_bounds)) \
$(subst .txt,%txt,$(iwasaki_27_30_te_data_table)) \
$(subst .txt,%txt,$(iwasaki_27_30_tr_bounds)) \
$(subst .txt,%txt,$(iwasaki_27_30_tr_data_table))
iwasaki_28_cts_by_codon = $(iwasaki_proc_dir)/cts_by_codon.size.28.28.txt
iwasaki_28_outputs = $(iwasaki_proc_dir)/outputs.size.28.28.txt
iwasaki_28_te_bounds = $(iwasaki_proc_dir)/te_set_bounds.size.28.28.trunc.20.20.min_cts.200.min_cod.100.top.300.txt
iwasaki_28_te_data_table = $(iwasaki_proc_dir)/te_set_bounds.size.28.28.trunc.20.20.min_cts.200.min_cod.100.top.300.data_table.txt
iwasaki_28_tr_bounds = $(iwasaki_proc_dir)/tr_set_bounds.size.28.28.trunc.20.20.min_cts.200.min_cod.100.top.300.txt
iwasaki_28_tr_data_table = $(iwasaki_proc_dir)/tr_set_bounds.size.28.28.trunc.20.20.min_cts.200.min_cod.100.top.300.data_table.txt
iwasaki_28_proc_sam_files = \
$(iwasaki_28_cts_by_codon) \
$(iwasaki_28_outputs) \
$(iwasaki_28_te_bounds) \
$(iwasaki_28_te_data_table) \
$(iwasaki_28_tr_bounds) \
$(iwasaki_28_tr_data_table)
iwasaki_28_proc_sam_pattern = \
$(subst .txt,%txt,$(iwasaki_28_cts_by_codon)) \
$(subst .txt,%txt,$(iwasaki_28_outputs)) \
$(subst .txt,%txt,$(iwasaki_28_te_bounds)) \
$(subst .txt,%txt,$(iwasaki_28_te_data_table)) \
$(subst .txt,%txt,$(iwasaki_28_tr_bounds)) \
$(subst .txt,%txt,$(iwasaki_28_tr_data_table))
leaveout_cods = $(shell seq -s ' ' -7 5)
iwasaki_full_model_files = \
$(foreach rep,$(10_reps),$(addprefix \
$(iwasaki_nn_dir)/full_cod_n5p4_nt_n15p14_rep$(rep)/,\
$(nn_70_epoch_files)))
iwasaki_full_model_pattern = \
$(addprefix $(iwasaki_nn_dir)/full_%/,$(nn_70_epoch_files))
iwasaki_exp_model_files = \
$(foreach rep,$(10_reps),$(addprefix \
$(iwasaki_nn_dir)/full_cod_n7p5_nt_n21p17_rep$(rep)/,\
$(nn_70_epoch_files)))
iwasaki_exp_model_pattern = \
$(addprefix $(iwasaki_nn_dir)/full_%/,$(nn_70_epoch_files))
iwasaki_leaveout_series_files = \
$(foreach lo_cod,$(leaveout_cods),\
$(foreach rep,$(10_reps), $(addprefix \
$(iwasaki_nn_dir)/nocod$(lo_cod)_cod_n7p5_nt_n21p17_rep$(rep)/,\
$(nn_70_epoch_files))))
iwasaki_leaveout_series_pattern = $(addprefix $(iwasaki_nn_dir)/nocod%/,\
$(nn_70_epoch_files))
iwasaki_28_files = $(addprefix $(iwasaki_nn_dir)/s28_cod_n5p4_nt_n15p14/,$(nn_70_epoch_files))
iwasaki_28_pattern = $(addprefix $(iwasaki_nn_dir)/s28_%/,$(nn_70_epoch_files))
iwasaki_full_plot_files = $(addprefix $(iwasaki_nn_dir)/full_cod_n5p4_nt_n15p14_rep0/plots/,$(nn_plot_files))
iwasaki_full_plot_pattern = $(addprefix $(iwasaki_nn_dir)/full_cod_n5p4_nt_n15p14_rep0/plot%/,$(nn_plot_files))
iwasaki_28_plot_files = $(addprefix $(iwasaki_nn_dir)/s28_cod_n5p4_nt_n15p14/plots/,$(nn_plot_files))
iwasaki_28_plot_pattern = $(addprefix $(iwasaki_nn_dir)/s28_cod_n5p4_nt_n15p14/plot%/,$(nn_plot_files))
iwasaki_feat_nb_series_num_epochs = 70
iwasaki_feat_nb_series_lr_decay = 32
iwasaki_feat_nb_series_num_reps = 10
iwasaki_leaveout_series_num_epochs = $(iwasaki_feat_nb_series_num_epochs)
iwasaki_leaveout_series_lr_decay = $(iwasaki_feat_nb_series_lr_decay)
iwasaki_leaveout_series_num_reps = $(iwasaki_feat_nb_series_num_reps)
iwasaki_28_num_epochs = 70
iwasaki_28_lr_decay = 32
iwasaki_28_num_reps = 10
# Iwasaki results files variable definitions
iwasaki_results_dir = $(results_dir)/iwasaki
iwasaki_results_feat_neighborhood_dir = \
$(iwasaki_results_dir)/feat_neighborhood_series
iwasaki_results_leaveout_dir = $(iwasaki_results_dir)/leaveout_series
iwasaki_results_full_dir = $(iwasaki_results_dir)/full_cod_n5p4_nt_n15p14_rep0
iwasaki_results_full_epoch_dir = $(iwasaki_results_full_dir)/epoch$(iwasaki_feat_nb_series_num_epochs)
iwasaki_results_28_dir = $(iwasaki_results_dir)/s28_cod_n5p4_nt_n15p14
iwasaki_results_28_epoch_dir = $(iwasaki_results_28_dir)/epoch$(iwasaki_28_num_epochs)
iwasaki_full_analysis_epoch_dir = $(iwasaki_nn_dir)/full_cod_n5p4_nt_n15p14_rep0/epoch$(iwasaki_feat_nb_series_num_epochs)
iwasaki_28_analysis_epoch_dir = $(iwasaki_nn_dir)/s28_cod_n5p4_nt_n15p14/epoch$(iwasaki_28_num_epochs)
iwasaki_full_codon_scores_results_files = \
$(iwasaki_results_full_epoch_dir)/codon_scores.tsv \
$(iwasaki_results_full_epoch_dir)/codon_scores_colormap.pdf
iwasaki_full_codon_scores_results_files_pattern = \
$(iwasaki_results_full_epoch_dir)/codon_scores%tsv \
$(iwasaki_results_full_epoch_dir)/codon_scores_colormap%pdf
iwasaki_28_codon_scores_results_files = \
$(iwasaki_results_28_epoch_dir)/codon_scores.tsv \
$(iwasaki_results_28_epoch_dir)/codon_scores_colormap.pdf
iwasaki_28_codon_scores_results_files_pattern = \
$(iwasaki_results_28_epoch_dir)/codon_scores%tsv \
$(iwasaki_results_28_epoch_dir)/codon_scores_colormap%pdf
iwasaki_feat_nb_corrs_file = \
$(iwasaki_results_feat_neighborhood_dir)/feat_neighborhood_corrs.txt
iwasaki_leaveout_mses_file = \
$(iwasaki_results_leaveout_dir)/leaveout_mses.txt
iwasaki_leaveout_corrs_file = \
$(iwasaki_results_leaveout_dir)/leaveout_corrs.txt
### Green variable definitions
green_expt_dir_name = green
green_expt_dir = $(expts_dir)/$(green_expt_dir_name)
green_proc_dir = $(green_expt_dir)/process
green_plot_dir = $(green_expt_dir)/plots
green_nn_dir = $(green_expt_dir)/lasagne_nn
green_lr_dir = $(green_expt_dir)/linreg
green_subdirs = $(addprefix $(green_expt_dir)/,$(expt_subdirs))
green_subdirs_pattern = $(addprefix $(green_expt_dir)%,$(expt_subdirs))
green_gene_len_file = $(genome_dir)/yeast_13cds10_lengths.txt
green_gene_seq_file = $(genome_dir)/yeast_13cds10.fa
green_raw_fastq_files = \
$(green_proc_dir)/SRR5008134.fastq \
$(green_proc_dir)/SRR5008135.fastq
green_trimmer_script = $(green_proc_dir)/trim_linker_green.pl
green_mapping_script = $(green_proc_dir)/green.sh
green_raw_sam_file = $(green_expt_dir)/process/green.transcript.sam
green_mapped_sam_file = $(green_expt_dir)/process/green.transcript.mapped.sam
green_sam_file = $(green_expt_dir)/process/green.transcript.mapped.wts.sam
green_plot_files = ${addprefix ${green_plot_dir}/,${plot_files}}
green_plot_files_pattern = \
${addprefix ${green_plot_dir}/,${plot_files_pattern}}
green_27_29_cts_by_codon = $(green_proc_dir)/cts_by_codon.size.27.29.txt
green_27_29_outputs = $(green_proc_dir)/outputs.size.27.29.txt
green_27_29_te_bounds = $(green_proc_dir)/te_set_bounds.size.27.29.trunc.20.20.min_cts.200.min_cod.100.top.500.txt
green_27_29_te_data_table = $(green_proc_dir)/te_set_bounds.size.27.29.trunc.20.20.min_cts.200.min_cod.100.top.500.data_table.txt
green_27_29_tr_bounds = $(green_proc_dir)/tr_set_bounds.size.27.29.trunc.20.20.min_cts.200.min_cod.100.top.500.txt
green_27_29_tr_data_table = $(green_proc_dir)/tr_set_bounds.size.27.29.trunc.20.20.min_cts.200.min_cod.100.top.500.data_table.txt
green_27_29_proc_sam_files = \
$(green_27_29_cts_by_codon) \
$(green_27_29_outputs) \
$(green_27_29_te_bounds) \
$(green_27_29_te_data_table) \
$(green_27_29_tr_bounds) \
$(green_27_29_tr_data_table)
green_27_29_proc_sam_pattern = \
$(subst .txt,%txt,$(green_27_29_cts_by_codon)) \
$(subst .txt,%txt,$(green_27_29_outputs)) \
$(subst .txt,%txt,$(green_27_29_te_bounds)) \
$(subst .txt,%txt,$(green_27_29_te_data_table)) \
$(subst .txt,%txt,$(green_27_29_tr_bounds)) \
$(subst .txt,%txt,$(green_27_29_tr_data_table))
green_28_cts_by_codon = $(green_proc_dir)/cts_by_codon.size.28.28.txt
green_28_outputs = $(green_proc_dir)/outputs.size.28.28.txt
green_28_te_bounds = $(green_proc_dir)/te_set_bounds.size.28.28.trunc.20.20.min_cts.200.min_cod.100.top.500.txt
green_28_te_data_table = $(green_proc_dir)/te_set_bounds.size.28.28.trunc.20.20.min_cts.200.min_cod.100.top.500.data_table.txt
green_28_tr_bounds = $(green_proc_dir)/tr_set_bounds.size.28.28.trunc.20.20.min_cts.200.min_cod.100.top.500.txt
green_28_tr_data_table = $(green_proc_dir)/tr_set_bounds.size.28.28.trunc.20.20.min_cts.200.min_cod.100.top.500.data_table.txt
green_28_proc_sam_files = \
$(green_28_cts_by_codon) \
$(green_28_outputs) \
$(green_28_te_bounds) \
$(green_28_te_data_table) \
$(green_28_tr_bounds) \
$(green_28_tr_data_table)
green_28_proc_sam_pattern = \
$(subst .txt,%txt,$(green_28_cts_by_codon)) \
$(subst .txt,%txt,$(green_28_outputs)) \
$(subst .txt,%txt,$(green_28_te_bounds)) \
$(subst .txt,%txt,$(green_28_te_data_table)) \
$(subst .txt,%txt,$(green_28_tr_bounds)) \
$(subst .txt,%txt,$(green_28_tr_data_table))
green_full_model_files = \
$(foreach rep,$(10_reps),$(addprefix \
$(green_nn_dir)/full_cod_n5p4_nt_n15p14_rep$(rep)/,\
$(nn_50_epoch_files)))
green_full_model_pattern = $(addprefix $(green_nn_dir)/full_%/,\
$(nn_50_epoch_files))
green_exp_model_files = \
$(foreach rep,$(10_reps),$(addprefix \
$(green_nn_dir)/full_cod_n7p5_nt_n21p17_rep$(rep)/,\
$(nn_50_epoch_files)))
green_exp_model_pattern = $(addprefix $(green_nn_dir)/full_%/,\
$(nn_50_epoch_files))
green_leaveout_series_files = \
$(foreach lo_cod,$(leaveout_cods),\
$(foreach rep,$(10_reps), $(addprefix \
$(green_nn_dir)/nocod$(lo_cod)_cod_n7p5_nt_n21p17_rep$(rep)/,\
$(nn_50_epoch_files))))
green_leaveout_series_pattern = $(addprefix $(green_nn_dir)/nocod%/,\
$(nn_50_epoch_files))
green_28_files = $(addprefix $(green_nn_dir)/s28_cod_n5p4_nt_n15p14/,\
$(nn_30_epoch_files))
green_28_pattern = $(addprefix $(green_nn_dir)/s28_%/,$(nn_30_epoch_files))
green_full_plot_files = $(addprefix $(green_nn_dir)/full_cod_n5p4_nt_n15p14_rep0/plots/,$(nn_plot_files))
green_full_plot_pattern = $(addprefix $(green_nn_dir)/full_cod_n5p4_nt_n15p14_rep0/plot%/,$(nn_plot_files))
green_28_plot_files = $(addprefix $(green_nn_dir)/s28_cod_n5p4_nt_n15p14/plots/,$(nn_plot_files))
green_28_plot_pattern = $(addprefix $(green_nn_dir)/s28_cod_n5p4_nt_n15p14/plot%/,$(nn_plot_files))
green_feat_nb_series_num_epochs = 50
green_feat_nb_series_lr_decay = 8
green_feat_nb_series_num_reps = 10
green_leaveout_series_num_epochs = $(green_feat_nb_series_num_epochs)
green_leaveout_series_lr_decay = $(green_feat_nb_series_lr_decay)
green_leaveout_series_num_reps = $(green_feat_nb_series_num_reps)
green_28_num_epochs = 30
green_28_lr_decay = 8
green_28_num_reps = 10
# Green results files variable definitions
green_results_dir = $(results_dir)/green
green_results_feat_neighborhood_dir = \
$(green_results_dir)/feat_neighborhood_series
green_results_leaveout_dir = $(green_results_dir)/leaveout_series
green_results_full_dir = $(green_results_dir)/full_cod_n5p4_nt_n15p14_rep0
green_results_full_epoch_dir = $(green_results_full_dir)/epoch$(green_feat_nb_series_num_epochs)
green_results_28_dir = $(green_results_dir)/s28_cod_n5p4_nt_n15p14
green_results_28_epoch_dir = $(green_results_28_dir)/epoch$(green_28_num_epochs)
green_full_analysis_epoch_dir = $(green_nn_dir)/full_cod_n5p4_nt_n15p14_rep0/epoch$(green_feat_nb_series_num_epochs)
green_28_analysis_epoch_dir = $(green_nn_dir)/s28_cod_n5p4_nt_n15p14/epoch$(green_28_num_epochs)
green_full_codon_scores_results_files = \
$(green_results_full_epoch_dir)/codon_scores.tsv \
$(green_results_full_epoch_dir)/codon_scores_colormap.pdf
green_full_codon_scores_results_files_pattern = \
$(green_results_full_epoch_dir)/codon_scores%tsv \
$(green_results_full_epoch_dir)/codon_scores_colormap%pdf
green_28_codon_scores_results_files = \
$(green_results_28_epoch_dir)/codon_scores.tsv \
$(green_results_28_epoch_dir)/codon_scores_colormap.pdf
green_28_codon_scores_results_files_pattern = \
$(green_results_28_epoch_dir)/codon_scores%tsv \
$(green_results_28_epoch_dir)/codon_scores_colormap%pdf
green_feat_nb_corrs_file = \
$(green_results_feat_neighborhood_dir)/feat_neighborhood_corrs.txt
green_leaveout_mses_file = \
$(green_results_leaveout_dir)/leaveout_mses.txt
green_leaveout_corrs_file = \
$(green_results_leaveout_dir)/leaveout_corrs.txt
### figure variable defintions
fig_files = \
$(fig_dir)/figure_1B_scaledcts.pdf \
$(fig_dir)/figure_1C_corrs.pdf \
$(fig_dir)/figure_1D_scatter.pdf \
$(fig_dir)/figure_1D_scatter_inset.pdf \
$(fig_dir)/figure_1E_indiv_gene.pdf \
$(fig_dir)/figure_1F_binned_error.pdf \
$(fig_dir)/figure_2A_downsampling.pdf \
$(fig_dir)/figure_2B_comparison.pdf \
$(fig_dir)/figure_3A_codoncorrs.pdf \
$(fig_dir)/figure_3B_heatmap.pdf \
$(fig_dir)/figure_3C_tai.pdf \
$(fig_dir)/figure_3C_wobble.pdf \
$(fig_dir)/figure_3D_lareaucodoncorrs.pdf \
$(fig_dir)/figure_3E_5prime.pdf \
$(fig_dir)/figure_3F_asite.pdf \
$(fig_dir)/figure_3G_cl2.pdf \
$(fig_dir)/figure_4B_citrine_dist.pdf \
$(fig_dir)/figure_4C_facs.pdf \
$(fig_dir)/figure_4D_te.pdf \
$(fig_dir)/supp_table_codon_scores.csv \
$(fig_dir)/supp_figure_mrna_qpcr.pdf \
$(fig_dir)/supp_figure_facs.pdf \
$(fig_dir)/supp_figure_greencorrs.pdf \
$(fig_dir)/supp_figure_iwasakicorrs.pdf \
$(fig_dir)/supp_figure_cl1.pdf \
$(fig_dir)/supp_figure_cl1v2.pdf \
$(fig_dir)/supp_figure_liu_subspace.pdf \
$(fig_dir)/supp_figure_a_site.pdf \
$(fig_dir)/supp_figure_contexts.pdf
# $(fig_dir)/figure_1C_mse.pdf
# $(fig_dir)/figure_3A_codonmse.pdf
# $(fig_dir)/figure_3E_lareaucodonmse.pdf
# $(fig_dir)/supp_figure_greenmse.pdf
# $(fig_dir)/supp_figure_iwasakimse.pdf
### paper data files
paper_data_dir = $(results_dir)/paper_data
paper_data_fname = $(paper_data_dir)/paper_data.txt
.PHONY: install expts weinberg_expt iwasaki_expt iwasaki_expt weinberg_clean figures
################################
### all: Overall make command
################################
all: install expts paper_data
##########################################################
### Installation: Build basic top level file structures
##########################################################
# NOTE: This is where I test definitions in the makefile
test:
echo $(weinberg_28_codon_scores_results_files_pattern)
# NOTE: Installation graveyard. Has been (mostly?) replaced by cloning git repo
#install: \
$(lib_files) \
$(genome_files) \
$(repro_files) \
$(struc_files) \
$(wetlab_files) \
$(results_dir) \
$(fig_dir) \
$(yeast_30_windows_seqs_file) \
$(yeast_30_windows_str_scores_file)
# Make main directory
$(top_dir):
mkdir $(top_dir)
#$(lib_dir): | $(top_dir)
# if ! [ -a $(lib_dir) ] ; then mkdir $(lib_dir) ; fi;
#$(genome_dir): | $(top_dir)
# mkdir $(genome_dir)