ADD : Add the option to use the defragmentation pipeline in 'workflow'

VERSION

@@ -1 +1 @@
-1.0.11
+1.0.12

ppanggolin/workflow/workflow.py

@@ -38,12 +38,12 @@ def launch(args):
             readClustering(pangenome, args.clusters)
 
         elif args.clusters is None:#we should have the sequences here.
-            clustering(pangenome, args.tmpdir, args.cpu)
+            clustering(pangenome, tmpdir = args.tmpdir, cpu = args.cpu, defrag = args.defrag)
     elif args.fasta is not None:
-            pangenome = Pangenome()
-            annotatePangenome(pangenome, args.fasta, args.tmpdir, args.cpu)
-            writePangenome(pangenome, filename, args.force)
-            clustering(pangenome, args.tmpdir, args.cpu)
+        pangenome = Pangenome()
+        annotatePangenome(pangenome, args.fasta, args.tmpdir, args.cpu)
+        writePangenome(pangenome, filename, args.force)
+        clustering(pangenome, tmpdir = args.tmpdir,cpu = args.cpu, defrag = args.defrag)
 
     computeNeighborsGraph(pangenome)
 
@@ -74,4 +74,5 @@ def workflowSubparser(subparser):
     optional.add_argument("--basename",required = False, default = "pangenome", help = "basename for the output file")
     optional.add_argument("--rarefaction", required=False, action = "store_true", help = "Use to compute the rarefaction curves (WARNING: can be time consumming)")
     optional.add_argument("-K","--nb_of_partitions",required=False, default=-1, type=int, help = "Number of partitions to use. Must be at least 3. If under 3, it will be detected automatically.")
+    optional.add_argument("--defrag",required=False, action="store_true", help = "Realign gene families to associated fragments with their non-fragmented gene family.")
     return parser