Merge pull request #1 from jbayer/master

Multifile pdf

src/enrichAnalysis.py

@@ -60,13 +60,12 @@ def main(mti_d = {}, rank_l = [], perm_num = 1000, p = 1, s_path = '', h_path =
 
     mir_l = mti_d.keys()
     mir_l.sort(key=ns.natural_keys)
-    es_plot_pages = PdfPages(e_path)
     es_q = Queue()
     proc_l = []
 
 # calculate ES + Leading Edge and NES #
     for mir in mir_l:    
-        es_ms = ms.Process(target=get_es, args=(mir,mti_d[mir], rank_l, perm_gene_l,p, n, perm_num, es_plot_pages, es_q))
+        es_ms = ms.Process(target=get_es, args=(mir,mti_d[mir], rank_l, perm_gene_l,p, n, perm_num, es_q))
         proc_l.append(es_ms)
         es_ms.start()
 
@@ -102,8 +101,9 @@ def main(mti_d = {}, rank_l = [], perm_num = 1000, p = 1, s_path = '', h_path =
             # Extend MTI-set-genes file #
             es_genes(mir, e[8], e[10], e[2], e[3], le_gene_file)
             # ES plot with all main running ESs  #
+            es_plot_pages = PdfPages(e_path+"-"+mir+".pdf")
             es_plot(mir, e[8], e[2], e[3]+1, e[9], e[10], e[11], es_plot_pages)
-    es_plot_pages.close()
+            es_plot_pages.close()
     le_gene_file.close()
 
 # calculate FDR q-value#
@@ -121,7 +121,7 @@ def main(mti_d = {}, rank_l = [], perm_num = 1000, p = 1, s_path = '', h_path =
 # create output #
     get_output(new_mti_d, max_es_d, max_es_ind_d, nes_d, FDR_mean_d, FDR_median_d, lead_edge_d, out_str, s_path)        
 
-def get_es(s, mti_l, rank_l, gene_l, p, n, perm_num, es_plot_pages, es_q):
+def get_es(s, mti_l, rank_l, gene_l, p, n, perm_num, es_q):
 
 
     n = float(n)    # number of genes in ranked list
@@ -214,7 +214,7 @@ def get_nes(max_es, nh, rank_l, gene_l, perm_num, p, n):
     for _ in range(0,perm_num):
         tmp_mti_l = random.sample(gene_l,nh) # randomly fill sets with same number of targets
     # new mti_dict done #
-        tmp_es = get_es('x', tmp_mti_l, rank_l, gene_l, p, n,False,False, None)
+        tmp_es = get_es('x', tmp_mti_l, rank_l, gene_l, p, n,False, None)
         perm_es_l.append(tmp_es)
         if tmp_es >= 0:
             perm_pos_es_l.append(tmp_es)

src/gsea.py

@@ -29,4 +29,4 @@
 except IOError as e:
 	print("Unable to open file "+sys.argv[2]+". File might not exist or missing read permissions.")
 
-enrichAnalysis.main(mti_d = genesets, rank_l = ranks, s_path = sys.argv[3]+'-genesets_ranked.txt', h_path = sys.argv[3]+'-geneset_overlap.pdf', e_path = sys.argv[3]+'-genesets.pdf', le_path = sys.argv[3]+'-geneset_genes.txt')
+enrichAnalysis.main(mti_d = genesets, rank_l = ranks, s_path = sys.argv[3]+'-genesets_ranked.txt', h_path = sys.argv[3]+'-geneset_overlap.pdf', e_path = sys.argv[3], le_path = sys.argv[3]+'-geneset_genes.txt')