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cobilab · Jul 27, 2023 · bd5116e · bd5116e
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Showing 4 changed files with 12 additions and 1 deletion.
diff --git a/benchmark/Download_FASTA.sh b/benchmark/Download_FASTA.sh
@@ -19,6 +19,12 @@ efetch -db nucleotide -id "NC_000024.1" -format fasta > CY.fa
 #
 # COPUS -----------------------------------------------------------------------
 #
-ls
+wget http://sweet.ua.pt/pratas/datasets/DNACorpus.zip
+unzip DNACorpus.zip
+cat DNACorpus/* | gto_fasta_from_seq -n "CORPUS" > CORPUS.fa
 #
 # -----------------------------------------------------------------------------
+#
+wget virus.fa
+#
+#
diff --git a/benchmark/Install_Tools.sh b/benchmark/Install_Tools.sh
@@ -1,5 +1,9 @@
 #!/bin/bash
 #
+# GTO TOOLKIT ------------------------------------------------------------------
+#
+conda install -y -c cobilab gto
+#
 # LZMA -------------------------------------------------------------------------
 #
 sudo apt-get install -y lzma

diff --git a/benchmark/Run_All_FASTA.sh b/benchmark/Run_All_FASTA.sh
@@ -4,4 +4,5 @@
 ./Benchmark_FASTA.sh CY.fa
 ./Benchmark_FASTA.sh CASSAVA.fa
 ./Benchmark_FASTA.sh HUMAN.fa
+./Benchmark_FASTA.sh CORPUS.fa
 #
diff --git a/benchmark/VIRUS_REFS_NCBI_15_JULY.fa.tar b/benchmark/VIRUS_REFS_NCBI_15_JULY.fa.tar