fix crazy cluster assignment bug in clustering step

labgem · Dec 16, 2021 · ed270c6 · ed270c6
1 parent 7d615f2
commit ed270c6
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Showing 2 changed files with 3 additions and 8 deletions.
diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-1.2.62
+1.2.63
diff --git a/ppanggolin/cluster/cluster.py b/ppanggolin/cluster/cluster.py
@@ -32,16 +32,11 @@ def alignRep(faaFile, tmpdir, cpu, coverage, identity):
     logging.getLogger().debug(" ".join(cmd))
     logging.getLogger().info("Aligning cluster representatives...")
     subprocess.run(cmd, stdout=subprocess.DEVNULL, check=True)
-    outdb = tmpdir.name + '/rep_families'
-    cmd = ["mmseqs", "convertalis", seqdb, seqdb, alndb, outdb, "--format-output", "target,qlen,tlen,bits", "--db-output","1"]
-    logging.getLogger().debug(" ".join(cmd))
-    logging.getLogger().info("Extracting alignments...")
-    subprocess.run(cmd, stdout=subprocess.DEVNULL, check=True)
     outfile = tmpdir.name + '/rep_families.tsv'
-    cmd = ["mmseqs","createtsv",seqdb, seqdb, outdb, outfile, "--full-header","1"]
+    cmd = ["mmseqs", "convertalis", seqdb, seqdb, alndb, outfile, "--format-output", "query,target,qlen,tlen,bits"]
     logging.getLogger().debug(" ".join(cmd))
+    logging.getLogger().info("Extracting alignments...")
     subprocess.run(cmd, stdout=subprocess.DEVNULL, check=True)
-
     return outfile