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dvc.yaml
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dvc.yaml
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stages:
sample proGenomes:
cmd: cargo run --release --manifest-path src/samplefa/Cargo.toml -- --input data/progenomes/freeze12.contigs.representatives.fasta.gz
--output data/progenomes/freeze12.contigs.representatives.randomly_selected.fasta
--seed 42 --min-size 250000 --total 5000
deps:
- data/progenomes/freeze12.contigs.representatives.fasta.gz
- src/samplefa/Cargo.lock
- src/samplefa/Cargo.toml
- src/samplefa/main.rs
outs:
- data/progenomes/freeze12.contigs.representatives.randomly_selected.fasta
deduplicate selected proGenomes contigs:
cmd: python -m src.dedupbyani --input data/progenomes/freeze12.contigs.representatives.randomly_selected.fasta
--list data/progenomes/freeze12.contigs.representatives.deduplicated.txt --6genomes
data/6genomes --9genomes data/9genomes --total 5000
deps:
- data/6genomes/Anabaena_variabilis_ATCC_29413_NC_007413.1.gbk
- data/6genomes/Pseudomonas_fluorescens_Pf-5_NC_004129.6.gbk
- data/6genomes/Saccharopolyspora_erythraea_NRRL_2338_AM420293.1.gbk
- data/6genomes/Salinispora_tropica_CNB-440_NC_009380.1.gbk
- data/6genomes/Sorangium_cellulosum_So_ce_56_AM746676.1.gbk
- data/6genomes/Streptomyces_griseus_griseus_NBRC_13350_AP009493.1.gbk
- data/9genomes/Kutzneria_sp_744_KK037166.1.gbk
- data/9genomes/Micromonospora_sp_ATCC_39149_GG657738.1.gbk
- data/9genomes/Micromonospora_sp_M42_KK037233.1.gbk
- data/9genomes/Streptomyces_albidoflavus_strain_J1074_DS999645.1.gbk
- data/9genomes/Streptomyces_ghanaensis_ATCC_14672_DS999641.1.gbk
- data/9genomes/Streptomyces_ghanaensis_ATCC_14672_DS999642.1.gbk
- data/9genomes/Streptomyces_hygroscopicus_ATCC_53653_GG657754.1.gbk
- data/9genomes/Streptomyces_pristinaespiralis_ATCC_25486_CM000950.1.gbk
- data/9genomes/Streptomyces_sp_AA4_GG657746.1.gbk
- data/9genomes/Streptomyces_sp_AA4_GG657747.1.gbk
- data/9genomes/Streptomyces_sp_C_GG657750.1.gbk
- data/9genomes/Streptomyces_sp_C_GG657751.1.gbk
- data/9genomes/Streptomyces_sp_C_GG657752.1.gbk
- data/progenomes/freeze12.contigs.representatives.randomly_selected.fasta
outs:
- data/progenomes/freeze12.contigs.representatives.deduplicated.txt:
cache: false
extract deduplicated proGenomes contigs:
cmd: cargo run --release --manifest-path src/extractfa/Cargo.toml -- --input data/progenomes/freeze12.contigs.representatives.fasta.gz
--list data/progenomes/freeze12.contigs.representatives.deduplicated.txt --output
data/progenomes/freeze12.contigs.representatives.deduplicated.fasta
deps:
- data/progenomes/freeze12.contigs.representatives.deduplicated.txt
- data/progenomes/freeze12.contigs.representatives.fasta.gz
outs:
- data/progenomes/freeze12.contigs.representatives.deduplicated.fasta
analyze deduplicated proGenomes contigs:
cmd: antismash -v --skip-zip-file --genefinding-tool prodigal-m --output-dir data/antismash/freeze12.contigs.representatives.deduplicated
--output-basename deduplicated data/progenomes/freeze12.contigs.representatives.deduplicated.fasta
deps:
- data/progenomes/freeze12.contigs.representatives.deduplicated.fasta
outs:
- data/antismash/freeze12.contigs.representatives.deduplicated/deduplicated.gbk
- data/antismash/freeze12.contigs.representatives.deduplicated/deduplicated.json
remove biosynthetic regions from proGenomes contigs:
cmd: python -m src.delregions --input data/antismash/freeze12.contigs.representatives.deduplicated/deduplicated.gbk
--list data/progenomes/freeze12.contigs.representatives.deduplicated.txt --output
data/progenomes/freeze12.contigs.representatives.cleaned.fasta
deps:
- data/antismash/freeze12.contigs.representatives.deduplicated/deduplicated.gbk
- data/progenomes/freeze12.contigs.representatives.deduplicated.txt
outs:
- data/progenomes/freeze12.contigs.representatives.cleaned.fasta
analyze cleaned proGenomes contigs:
cmd: antismash -v --skip-zip-file --genefinding-tool prodigal-m --output-dir data/antismash/freeze12.contigs.representatives.cleaned
--output-basename cleaned data/progenomes/freeze12.contigs.representatives.cleaned.fasta
deps:
- data/progenomes/freeze12.contigs.representatives.cleaned.fasta
outs:
- data/antismash/freeze12.contigs.representatives.cleaned/cleaned.gbk
- data/antismash/freeze12.contigs.representatives.cleaned/cleaned.json
make MIBiG_1_3 embeddings:
cmd: python -m src.embed --input data/antismash/freeze12.contigs.representatives.cleaned/cleaned.gbk
--list data/progenomes/freeze12.contigs.representatives.deduplicated.txt --mibig
data/mibig/ --version 1.3 --output-prefix data/embeddings/mibig-1.3.proG2 --retire
data/mibig/retire.txt
deps:
- data/antismash/freeze12.contigs.representatives.cleaned/cleaned.gbk
- data/mibig/mibig-1.3.gbk.tar.gz
- data/mibig/mibig-1.3.json.tar.gz
- data/mibig/mibig-1.4.json.tar.gz
- data/mibig/mibig-2.0.json.tar.gz
- data/mibig/retire.txt
- data/progenomes/freeze12.contigs.representatives.deduplicated.txt
outs:
- data/embeddings/mibig-1.3.proG2.clusters.tsv:
cache: false
- data/embeddings/mibig-1.3.proG2.fna
- data/embeddings/mibig-1.3.proG2.gbk
make MIBiG_2_0 embeddings:
cmd: python -m src.embed --input data/antismash/freeze12.contigs.representatives.cleaned/cleaned.gbk
--list data/progenomes/freeze12.contigs.representatives.deduplicated.txt --mibig
data/mibig/ --version 2.0 --output-prefix data/embeddings/mibig-2.0.proG2 --retire
data/mibig/retire.txt
deps:
- data/antismash/freeze12.contigs.representatives.cleaned/cleaned.gbk
- data/mibig/mibig-1.3.json.tar.gz
- data/mibig/mibig-1.4.json.tar.gz
- data/mibig/mibig-2.0.gbk.tar.gz
- data/mibig/mibig-2.0.json.tar.gz
- data/mibig/retire.txt
- data/progenomes/freeze12.contigs.representatives.deduplicated.txt
outs:
- data/embeddings/mibig-2.0.proG2.clusters.tsv:
cache: false
- data/embeddings/mibig-2.0.proG2.fna
- data/embeddings/mibig-2.0.proG2.gbk
index MIBiG_1_3 FASTA embedding:
cmd: samtools faidx data/embeddings/mibig-1.3.proG2.fna
deps:
- data/embeddings/mibig-1.3.proG2.fna
outs:
- data/embeddings/mibig-1.3.proG2.fna.fai
index MIBiG_2_0 FASTA embedding:
cmd: samtools faidx data/embeddings/mibig-2.0.proG2.fna
deps:
- data/embeddings/mibig-2.0.proG2.fna
outs:
- data/embeddings/mibig-2.0.proG2.fna.fai
annotate MIBiG_1_3 embeddings with Pfam_33_1:
cmd: src/annotate/gecco-annotate-slurm.sh data/embeddings/mibig-1.3.proG2.fna.fai
data/hmms/Pfam-v33.1.hmm.gz
deps:
- data/embeddings/mibig-1.3.proG2.fna.fai
- data/hmms/Pfam-v33.1.hmm.gz
outs:
- data/embeddings/mibig-1.3.proG2.Pfam-v33.1.features.tsv
annotate MIBiG_1_3 embeddings with Pfam_34_0:
cmd: src/annotate/gecco-annotate-slurm.sh data/embeddings/mibig-1.3.proG2.fna.fai
data/hmms/Pfam-v34.0.hmm.gz
deps:
- data/embeddings/mibig-1.3.proG2.fna.fai
- data/hmms/Pfam-v34.0.hmm.gz
outs:
- data/embeddings/mibig-1.3.proG2.Pfam-v34.0.features.tsv
annotate MIBiG_1_3 embeddings with Tigrfam_15_0:
cmd: src/annotate/gecco-annotate-slurm.sh data/embeddings/mibig-1.3.proG2.fna.fai
data/hmms/Tigrfam-v15.0.hmm.gz
deps:
- data/embeddings/mibig-1.3.proG2.fna.fai
- data/hmms/Tigrfam-v15.0.hmm.gz
outs:
- data/embeddings/mibig-1.3.proG2.Tigrfam-v15.0.features.tsv
annotate MIBiG_1_3 embeddings with Pfam_31_0:
cmd: src/annotate/gecco-annotate-slurm.sh data/embeddings/mibig-1.3.proG2.fna.fai
data/hmms/Pfam-v31.0.hmm.gz
deps:
- data/embeddings/mibig-1.3.proG2.fna.fai
- data/hmms/Pfam-v31.0.hmm.gz
outs:
- data/embeddings/mibig-1.3.proG2.Pfam-v31.0.features.tsv
annotate MIBiG_2_0 embeddings with Tigrfam_15_0:
cmd: src/annotate/gecco-annotate-slurm.sh data/embeddings/mibig-2.0.proG2.fna.fai
data/hmms/Tigrfam-v15.0.hmm.gz
deps:
- data/embeddings/mibig-2.0.proG2.fna.fai
- data/hmms/Tigrfam-v15.0.hmm.gz
outs:
- data/embeddings/mibig-2.0.proG2.Tigrfam-v15.0.features.tsv
annotate MIBiG_2_0 embeddings with Pfam_31_0:
cmd: src/annotate/gecco-annotate-slurm.sh data/embeddings/mibig-2.0.proG2.fna.fai
data/hmms/Pfam-v31.0.hmm.gz
deps:
- data/embeddings/mibig-2.0.proG2.fna.fai
- data/hmms/Pfam-v31.0.hmm.gz
outs:
- data/embeddings/mibig-2.0.proG2.Pfam-v31.0.features.tsv
annotate MIBiG_2_0 embeddings with Pfam_33_1:
cmd: src/annotate/gecco-annotate-slurm.sh data/embeddings/mibig-2.0.proG2.fna.fai
data/hmms/Pfam-v33.1.hmm.gz
deps:
- data/embeddings/mibig-2.0.proG2.fna.fai
- data/hmms/Pfam-v33.1.hmm.gz
outs:
- data/embeddings/mibig-2.0.proG2.Pfam-v33.1.features.tsv
annotate MIBiG_2_0 embeddings with Pfam_34_0:
cmd: src/annotate/gecco-annotate-slurm.sh data/embeddings/mibig-2.0.proG2.fna.fai
data/hmms/Pfam-v34.0.hmm.gz
deps:
- data/embeddings/mibig-2.0.proG2.fna.fai
- data/hmms/Pfam-v34.0.hmm.gz
outs:
- data/embeddings/mibig-2.0.proG2.Pfam-v34.0.features.tsv
annotate MIBiG_1_3 embeddings with Pfam_35_0:
cmd: src/annotate/gecco-annotate-slurm.sh data/embeddings/mibig-1.3.proG2.fna.fai
data/hmms/Pfam-v35.0.hmm.gz
deps:
- data/embeddings/mibig-1.3.proG2.fna.fai
- data/hmms/Pfam-v35.0.hmm.gz
outs:
- data/embeddings/mibig-1.3.proG2.Pfam-v35.0.features.tsv
annotate MIBiG_2_0 embeddings with Pfam_35_0:
cmd: src/annotate/gecco-annotate-slurm.sh data/embeddings/mibig-2.0.proG2.fna.fai
data/hmms/Pfam-v35.0.hmm.gz
deps:
- data/embeddings/mibig-2.0.proG2.fna.fai
- data/hmms/Pfam-v35.0.hmm.gz
outs:
- data/embeddings/mibig-2.0.proG2.Pfam-v35.0.features.tsv