Prepare feature tables for Pfam v35.0

zellerlab · Mar 20, 2022 · 7c920de · 7c920de
1 parent b116299
commit 7c920de
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diff --git a/data/embeddings/.gitignore b/data/embeddings/.gitignore
@@ -14,3 +14,5 @@
 /mibig-2.0.proG2.Pfam-v34.0.features.tsv
 /mibig-1.3.proG2.genes.gff
 /mibig-2.0.proG2.genes.gff
+/mibig-1.3.proG2.Pfam-v35.0.features.tsv
+/mibig-2.0.proG2.Pfam-v35.0.features.tsv
diff --git a/dvc.lock b/dvc.lock
@@ -354,3 +354,31 @@ stages:
  - path: data/embeddings/mibig-2.0.proG2.Pfam-v34.0.features.tsv
  md5: 1cf574cdd7edac64be3585631949b8f1
  size: 1394084376
+ 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:
+ - path: data/embeddings/mibig-1.3.proG2.fna.fai
+ md5: 09380d57c4651a389839cb009ee11845
+ size: 77224
+ - path: data/hmms/Pfam-v35.0.hmm.gz
+ md5: 2cdbfbec0e3c6f0b1ecb6db1b8fc337f
+ size: 293000230
+ outs:
+ - path: data/embeddings/mibig-1.3.proG2.Pfam-v35.0.features.tsv
+ md5: dbeb21021e02d3565504f64ac8e11a05
+ size: 1219655461
+ 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:
+ - path: data/embeddings/mibig-2.0.proG2.fna.fai
+ md5: bcd11573d7e46b306781770875f2b02b
+ size: 105772
+ - path: data/hmms/Pfam-v35.0.hmm.gz
+ md5: 2cdbfbec0e3c6f0b1ecb6db1b8fc337f
+ size: 293000230
+ outs:
+ - path: data/embeddings/mibig-2.0.proG2.Pfam-v35.0.features.tsv
+ md5: 74897a4da58e6187c4840df0f85f17b8
+ size: 1686462239
diff --git a/dvc.yaml b/dvc.yaml
@@ -184,3 +184,19 @@ stages:
  - 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