search reference proteomes

rnabioco · May 20, 2024 · 71bc3df · 71bc3df
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diff --git a/results/2024-05-20/hmmesearch-ref-proteomes.816252.errout b/results/2024-05-20/hmmesearch-ref-proteomes.816252.errout
@@ -0,0 +1,6 @@
++ class=class-2
++ project=/beevol/home/jhessel/devel/rnabioco/2a-peptide-search
++ hmm=/beevol/home/jhessel/devel/rnabioco/2a-peptide-search/curated-models/2A-class-2.hmm
++ seq=/beevol/home/jhessel/devel/rnabioco/2a-peptide-search/data/ref/uniprot/reference_proteomes/reference_proteomes.fasta.gz
++ hmmsearch --tblout ref-proteomes.class-2.hmmsearch.tab -A ref-proteomes.class-2.sto --noali /beevol/home/jhessel/devel/rnabioco/2a-peptide-search/curated-models/2A-class-2.hmm /beevol/home/jhessel/devel/rnabioco/2a-peptide-search/data/ref/uniprot/reference_proteomes/reference_proteomes.fasta.gz
++ gzip -c
diff --git a/results/2024-05-20/ref-proteomes.class-1.hmmsearch.gz b/results/2024-05-20/ref-proteomes.class-1.hmmsearch.gz
diff --git a/results/2024-05-20/ref-proteomes.class-1.hmmsearch.tab.gz b/results/2024-05-20/ref-proteomes.class-1.hmmsearch.tab.gz
diff --git a/results/2024-05-20/ref-proteomes.class-1.sto.gz b/results/2024-05-20/ref-proteomes.class-1.sto.gz
diff --git a/results/2024-05-20/ref-proteomes.class-2.hmmsearch.gz b/results/2024-05-20/ref-proteomes.class-2.hmmsearch.gz
diff --git a/results/2024-05-20/ref-proteomes.class-2.hmmsearch.tab.gz b/results/2024-05-20/ref-proteomes.class-2.hmmsearch.tab.gz
diff --git a/results/2024-05-20/ref-proteomes.class-2.sto.gz b/results/2024-05-20/ref-proteomes.class-2.sto.gz
diff --git a/results/2024-05-20/run.sh b/results/2024-05-20/run.sh
@@ -0,0 +1,18 @@
+#! /usr/bin/env bash
+
+#BSUB -J hmmsearch[1-2]
+#BSUB -eo hmmesearch-ref-proteomes.%J.errout
+
+set -x
+
+class="class-$LSB_JOBINDEX"
+project=$HOME/devel/rnabioco/2a-peptide-search
+hmm="$project/curated-models/2A-$class.hmm"
+seq=$project/data/ref/uniprot/reference_proteomes/reference_proteomes.fasta.gz
+
+hmmsearch  \
+    --tblout ref-proteomes.$class.hmmsearch.tab \
+    -A ref-proteomes.$class.sto \
+    --noali \
+    $hmm $seq \
+    | gzip -c > ref-proteomes.$class.hmmsearch.gz