# HG changeset patch
# User tyty
# Date 1413785496 14400
# Node ID 52b0eb6bef3153f0b184004ed535b3532586381d
# Parent  42b0b1e0e696f9f4e7a400a62ddbaffd197e7398
Deleted selected files

diff -r 42b0b1e0e696 -r 52b0eb6bef31 get_reads/predict_RNAs.py
--- a/get_reads/predict_RNAs.py	Mon Oct 20 02:11:19 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,93 +0,0 @@
-#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()
-    
-    
-
-
-