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dvc.yaml
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stages:
get_raw_data_taxa:
cmd: python pipeline/s0.0_get_raw_data_taxa.py
deps:
- pipeline/s0.0_get_raw_data_taxa.py
outs:
- ./data/taxa.parquet
params:
- get_raw_data_taxa.max_16s_len
- get_raw_data_taxa.min_16s_len
metrics:
- ./data/metrics/s0.0_metrics.yaml:
cache: false
get_raw_data_proteins:
cmd: python pipeline/s0.1_get_raw_data_proteins.py
deps:
- ./pipeline/s0.1_get_raw_data_proteins.py
outs:
- ./data/uniprot/uniprot_pulled_timestamp
params:
- get_raw_data_proteins.dev_only_one_uniprot_file
metrics:
- ./data/metrics/s0.1_metrics.yaml:
cache: false
get_proteome_mdata:
cmd: python pipeline/s0.2_get_proteome_mdata.py
deps:
- pipeline/s0.2_get_proteome_mdata.py
outs:
- ./data/uniprot/proteome_metadata.csv
parse_proteins:
cmd: python pipeline/s0.3_parse_proteins.py
deps:
- ./data/taxa.parquet
- ./data/uniprot/proteome_metadata.csv
- ./data/uniprot/uniprot_pulled_timestamp
- ./learn2therm/io.py
- ./pipeline/s0.3_parse_proteins.py
outs:
- ./data/metrics/s0.3_protein_per_data_distr.csv
- ./data/proteins/
params:
- parse_proteins.dev_only_one_uniprot_file
- parse_proteins.max_prot_per_file
metrics:
- ./data/metrics/s0.3_metrics.yaml:
cache: false
label_taxa:
cmd: python pipeline/s1.0_label_taxa.py
deps:
- ./data/taxa.parquet
- ./learn2therm/utils.py
- pipeline/s1.0_label_taxa.py
params:
- label_taxa.ogt_threshold
outs:
- ./data/taxa_thermophile_labels.parquet
metrics:
- ./data/metrics/s1.0_metrics.yaml:
cache: false
plots:
- ./data/plots/ogt_hist.png:
cache: false
get_16s_blast_scores:
cmd: python pipeline/s1.1_get_16s_blast_scores.py
deps:
- ./data/metrics/s0.3_protein_per_data_distr.csv
- ./data/taxa.parquet
- ./data/taxa_thermophile_labels.parquet
- ./learn2therm/blast.py
- ./learn2therm/io.py
- ./learn2therm/utils.py
- ./pipeline/s1.1_get_16s_blast_scores.py
outs:
- ./data/taxa_pairs/alignment/
params:
- get_16s_blast_scores.blast_metrics
- get_16s_blast_scores.dev_n_sample
- get_16s_blast_scores.gapextend_penalty
- get_16s_blast_scores.gapopen_penalty
- get_16s_blast_scores.num_threads
- get_16s_blast_scores.penalty
- get_16s_blast_scores.reward
- get_16s_blast_scores.ungapped
- get_16s_blast_scores.word_size
metrics:
- ./data/metrics/s1.1_metrics.yaml:
cache: false
label_all_pairs:
cmd: python pipeline/s1.2_label_all_pairs.py
deps:
- ./data/taxa_pairs/alignment
- ./learn2therm/utils.py
- ./pipeline/s1.2_label_all_pairs.py
outs:
- ./data/taxa_pairs/pair_labels
params:
- label_all_pairs.blast_metric_thresholds
- label_all_pairs.dev_only_one_file
metrics:
- ./data/metrics/s1.2_metrics.yaml:
cache: false
protein_alignment:
cmd: python ./pipeline/s1.3_protein_alignment.py
deps:
- ./data/proteins
- ./data/taxa_pairs/alignment
- ./data/taxa_pairs/pair_labels
- ./learn2therm/blast.py
- ./pipeline/s1.3_protein_alignment.py
params:
- get_protein_blast_scores.dask_cluster_class
- get_protein_blast_scores.dev_sample_pairs
- get_protein_blast_scores.max_protein_length
- get_protein_blast_scores.method
- get_protein_blast_scores.method_blast_params
- get_protein_blast_scores.method_diamond_params
- get_protein_blast_scores.n_jobs
- get_protein_blast_scores.save_frequency
outs:
- ./data/protein_pairs/:
checkpoint: true
metrics:
- ./data/metrics/s1.3_metrics.yaml:
cache: false
persist: true
make_database:
cmd: python ./pipeline/s1.4_make_database.py
deps:
- ./data/protein_pairs
- ./data/proteins
- ./data/taxa.parquet
- ./data/taxa_pairs/alignment
- ./data/taxa_pairs/pair_labels
- ./data/taxa_thermophile_labels.parquet
- ./learn2therm/database.py
outs:
- ./data/database.ddb
get_hait_pairs:
cmd: python ./pipeline/s2.1_get_hait_pairs.py
deps:
- ./pipeline/s2.1_get_hait_pairs.py
outs:
- ./data/validation/hait_pairs.csv
compare_to_Tm:
cmd: python ./pipeline/s2.2_compare_to_Tm.py
deps:
- ./data/database.ddb
- ./pipeline/s2.2_compare_to_Tm.py
outs:
- ./data/validation/tm/ogt_vs_tm.csv
metrics:
- ./data/validation/tm/metrics.yaml:
cache: false
plots:
- ./data/validation/tm/ogt_vs_tm_check.png:
cache: false
run_hait_alignment:
cmd: python ./pipeline/s2.3_run_hait_alignment.py
deps:
- ./pipeline/s2.3_run_hait_alignment.py
- ./learn2therm/blast.py
- ./data/validation/hait_pairs.csv
outs:
- ./data/validation/hait_aligned_scores.csv
params:
- get_protein_blast_scores.method
- get_protein_blast_scores.method_blast_params
- get_protein_blast_scores.method_diamond_params
compare_hait_alignment:
cmd: python ./pipeline/s2.4_compare_hait_alignment.py
deps:
- ./pipeline/s2.4_compare_hait_alignment.py
- ./data/validation/hait_aligned_scores.csv
- ./data/database.ddb
plots:
- ./data/validation/hait_alignment/:
cache: false
get_HMM_profiles:
cmd: python ./pipeline/s2.5_get_HMM_profiles.py
outs:
- ./data/validation/hmmer/Pfam-A.hmm
metrics:
- ./data/validation/hmmer/s2.5_metrics.yaml:
cache: false
hmmer_hait:
cmd: python ./pipeline/s2.6_hmmer_hait.py
deps:
- ./pipeline/s2.6_hmmer_hait.py
- ./data/validation/hmmer/Pfam-A.hmm
- ./data/validation/hait_pairs.csv
- ./learn2therm/hmmer.py
outs:
- ./data/validation/hmmer/hait_scores.csv
params:
- run_hmmer.e_value
- run_hmmer.njobs
- run_hmmer.jaccard_threshold
plots:
- ./data/validation/hmmer/hait_jaccard.png:
cache: false
- ./data/validation/hmmer/hait_n_domains.png:
cache: false
metrics:
- ./data/validation/hmmer/s2.6_metrics.yaml:
cache: false
run_hmmer:
cmd: python ./pipeline/s2.7_run_hmmer.py
deps:
- ./pipeline/s2.7_run_hmmer.py
- ./data/validation/hmmer/Pfam-A.hmm
- ./data/database.ddb
- ./learn2therm/hmmer.py
outs:
- ./data/validation/hmmer/hmmer_outputs/
params:
- run_hmmer.e_value
- run_hmmer.njobs
- run_hmmer.chunk_size
- run_hmmer.scan
- run_hmmer.dev_sample_data
- run_hmmer.prefetch
metrics:
- ./data/validation/hmmer/s2.7_metrics.yaml:
cache: false
parse_hmmer_result:
cmd: python ./pipeline/s2.8_parse_hmmer_result.py
deps:
- ./pipeline/s2.8_parse_hmmer_result.py
- ./data/validation/hmmer/hmmer_outputs/
- ./learn2therm/hmmer.py
- ./data/protein_pairs/
outs:
- ./data/validation/hmmer/hmmer_labels/
params:
- run_hmmer.jaccard_threshold
- run_hmmer.chunk_size
metrics:
- ./data/validation/hmmer/s2.8_metrics.yaml:
cache: false
compare_hait_hmmer:
cmd: python ./pipeline/s2.9_compare_hait_hmmer.py
deps:
- ./pipeline/s2.9_compare_hait_hmmer.py
- ./data/validation/hmmer/hmmer_labels/
- ./data/database.ddb
metrics:
- ./data/validation/hmmer/s2.9_metrics.yaml:
cache: false
plots:
- ./data/validation/hmmer/compare_jaccard_hist.png:
cache: false
sample_data_for_structure:
cmd: python ./pipeline/s2.10_sample_data_for_structure.py
deps:
- ./pipeline/s2.10_sample_data_for_structure.py
- ./data/database.ddb
outs:
- ./data/validation/structure/sample_l2t_data.csv
params:
- sample_data_for_structure.sample_size
- sample_data_for_structure.metrics
structure_hait:
cmd: python ./pipeline/s2.11_structure_hait.py
deps:
- ./pipeline/s2.11_structure_hait.py
- ./data/validation/hait_pairs.csv
outs:
- ./data/validation/structure/hait_fatcat.csv
structure_l2t:
cmd: python ./pipeline/s2.12_structure_l2t.py
deps:
- ./pipeline/s2.12_structure_l2t.py
- ./data/validation/structure/sample_l2t_data.csv
outs:
- ./data/validation/structure/l2t_sample_fatcat.csv
engqvist:
cmd: python ./pipeline/s2.13_map_to_engqvist.py
deps:
- ./pipeline/s2.13_map_to_engqvist.py
- ./data/database.ddb
metrics:
- ./data/validation/engqvist/metrics.yaml:
cache: false
plots:
- ./data/validation/engqvist/ogt_comparison.png:
cache: false