Update pseudo_pool.smk

rules/pseudo_pool.smk

@@ -10,22 +10,40 @@ def partition (list_in, n):  # Function to do random pooling
     return [list_in[i::n] for i in range(n)]
 
 #n_sb = 5
-n_cells = 15 
+if "n_pseudo_bulks" in config:
+    n_cells = int(config["n_pseudo_bulks"])
+else:
+    n_cells = 15 
 
 cluster_files_pb = dict()
 sb_IDs = set()
 
 for cluster, files in cluster_files.items():
     sb = 1
     n_sb = round(len(files)/n_cells)
-    print(cluster, len(files), n_sb)
-
+    if n_sb<3:
+        n_sb=3
+
     for pool in partition(files, n_sb):
         cluster_files_pb[(cluster, sb)] = pool
-	sb_IDs.add(cluster + "_" + str(sb))
+	    sb_IDs.add(cluster + "_" + str(sb))
         sb += 1
 
-
+rule get_pseudo_bulk_membership:
+    output:
+        table = "Whippet/Quant/Single_Cell/Pseudo_bulks/pseudo_bulk_membership.tsv"
+    run:
+        with open(output.table, "w") as out:
+            writer = csv.writer(out, delimiter='\t')
+            writer.writerow(["pseudo_bulk_ID", "samples"])
+
+            for key in cluster_files_pb:
+                cluster, sb = key
+                sb_ID = cluster + "_" + str(sb)
+                samples = ",".join(cluster_files_pb[key])
+                writer.writerow([sb_ID, samples])
+
+
 def get_files_by_cluster_pb(cluster, pool_ID):
     ext = ".fastq.gz"
     path="FASTQ/"
@@ -60,7 +78,8 @@ rule collapse_pseudo_pools:
   input: 
       gene = "Whippet/Quant/Single_Cell/Pseudo_bulks/pseudo_bulks.gene.tpm.tsv",
       isoform = "Whippet/Quant/Single_Cell/Pseudo_bulks/pseudo_bulks.isoform.tpm.tsv",
-      psi =  "Whippet/Quant/Single_Cell/Pseudo_bulks/pseudo_bulks.psi.tsv"
+      psi =  "Whippet/Quant/Single_Cell/Pseudo_bulks/pseudo_bulks.psi.tsv",
+      table =  "Whippet/Quant/Single_Cell/Pseudo_bulks/pseudo_bulk_membership.tsv"
 
 
 rule merge_quant_gene_sp: