pre-make RepeatPeps

CSU-KangHu · Jan 22, 2024 · 2b4a1d9 · 2b4a1d9
1 parent 05d126d
commit 2b4a1d9
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Showing 8 changed files with 24 additions and 2 deletions.
diff --git a/data/RepeatPeps.lib.pdb b/data/RepeatPeps.lib.pdb
diff --git a/data/RepeatPeps.lib.phr b/data/RepeatPeps.lib.phr
diff --git a/data/RepeatPeps.lib.pin b/data/RepeatPeps.lib.pin
diff --git a/data/RepeatPeps.lib.pjs b/data/RepeatPeps.lib.pjs
@@ -0,0 +1,22 @@
+{
+  "version": "1.2",
+  "dbname": "RepeatPeps.lib",
+  "dbtype": "Protein",
+  "db-version": 5,
+  "description": "/home/hukang/NeuralTE/configs/../data/RepeatPeps.lib",
+  "number-of-letters": 16150283,
+  "number-of-sequences": 18011,
+  "last-updated": "2024-01-17T22:35:00",
+  "number-of-volumes": 1,
+  "bytes-total": 19568986,
+  "bytes-to-cache": 16312527,
+  "files": [
+    "RepeatPeps.lib.pdb",
+    "RepeatPeps.lib.phr",
+    "RepeatPeps.lib.pin",
+    "RepeatPeps.lib.pot",
+    "RepeatPeps.lib.psq",
+    "RepeatPeps.lib.ptf",
+    "RepeatPeps.lib.pto"
+  ]
+}
diff --git a/data/RepeatPeps.lib.psq b/data/RepeatPeps.lib.psq
diff --git a/data/RepeatPeps.lib.ptf b/data/RepeatPeps.lib.ptf
diff --git a/data/RepeatPeps.lib.pto b/data/RepeatPeps.lib.pto
diff --git a/utils/data_util.py b/utils/data_util.py
@@ -927,8 +927,8 @@ def get_domain_info(cons, lib, output_table, threads, temp_dir):
         os.system('rm -rf ' + temp_dir)
     os.makedirs(temp_dir)
 
-    blast_db_command = 'makeblastdb -dbtype prot -in ' + lib
-    os.system(blast_db_command)
+    # blast_db_command = 'makeblastdb -dbtype prot -in ' + lib
+    # os.system(blast_db_command)
     # 1. Divide the cons, and for each block, use blastx -num_threads 1 -evalue 1e-20 to compare cons with domain.
     partitions_num = int(threads)
     consensus_contignames, consensus_contigs = read_fasta(cons)