changeset 17:42b0b1e0e696 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_reads/predict_RNAs.py	Mon Oct 20 02:11:19 2014 -0400
@@ -0,0 +1,93 @@
+#RNA structure prediction & Output and illustrate reactivities
+
+import sys
+from parse_dis_pac import *
+from read_file import *
+from Bio import SeqIO
+import os
+from rtts_plot import *
+
+
+id_file = sys.argv[1]
+seq_file = sys.argv[2]
+output_file = sys.argv[4]
+
+
+flag = 0
+if sys.argv[3]!='None': #input reactivity file if provided
+    react_file = sys.argv[3]
+    react = parse_dist(react_file)
+    react = react[1]
+    flag = 1
+
+ospath = os.path.realpath(sys.argv[0])
+ost = ospath.split('/')
+syspath = ""
+for i in range(len(ost)-1):
+    syspath = syspath+ost[i].strip()
+    syspath = syspath+'/' 
+
+ids = read_t_file(id_file)
+sequences = SeqIO.parse(seq_file, 'fasta')
+
+
+seqs = {}
+for seq in sequences:
+    seqs[seq.id] = seq.seq.tostring()
+
+if len(ids)>10: #setup a limit of the number of sequence to be predicted
+    print("Number of sequences exceeds limitation!")
+    sys.exit(0)
+    
+
+#predict RNA structures
+os.system("mkdir "+syspath+"output_f")
+for i in range(len(ids)):
+    id_s = ids[i][0]
+    print(id_s)
+    #Put RNA sequence and reactivities into files
+    if id_s in seqs:
+        f = file(syspath+"temp.txt", 'w')        
+        f.write('>'+id_s)
+        f.write('\n')
+        f.write(seqs[id_s])
+        f.close()
+        if flag == 0:
+            os.system("Fold "+syspath+"temp.txt"+" "+syspath+"output_f/"+id_s+".ct")
+        if flag == 1:
+            if id_s in react:
+                f = file(syspath+"constraint.txt",'w')
+                make_plot(react[id_s],id_s,(syspath+"output_f/")) #make a plot of the distribution of the reactivites of the input RNA
+                #h = file(syspath+"output_f/transcript_reactivities.txt", 'w')
+                #h.write(id_s)
+                #h.write('\n')
+                for j in range(0, (len(react[id_s]))):
+                    if react[id_s][j]!='NA':
+                        f.write(str(j+1))
+                        f.write('\t')
+                        f.write(str(react[id_s][j]))
+                        f.write('\n')
+                    #h.write(str(react[id_s][j])) #Output the reactivities
+                    #h.write('\t')
+                f.close()
+                #h.write('\n')
+                #h.write('\n')
+                os.system("Fold "+syspath+"temp.txt"+" -sh"+" "+syspath+"constraint.txt"+" "+syspath+"output_f/"+id_s+".ct")
+            else:
+                print(id_s+" not in the data of react!")
+        os.system("draw "+syspath+"output_f/"+id_s+".ct "+syspath+"output_f/"+id_s+".ps")
+    else:
+        print(id_s+" not in the data of sequences!")
+
+#Remove the unnecessary files
+os.system("tar -zcvPf "+output_file+" "+syspath+"output_f/"+"*.* 2>"+syspath+"log.txt")
+os.system("rm -f "+syspath+"temp.txt")
+os.system("rm -r "+syspath+"output_f")
+if flag == 1:
+    os.system("rm -f "+syspath+"constraint.txt")
+ #   h.close()
+    
+    
+
+
+