changeset 11:a71c7f99c92e draft

Deleted selected files

--- a/reactivity_cal/react_cal.py	Mon Oct 20 01:43:30 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,136 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-import sys
-from Bio import SeqIO
-import math
-from parse_dis_react import *
-from react_norm_function import *
-import os
-
-
-dist_file1 = sys.argv[1] #plus library
-dist_file2 = sys.argv[2] #minus library
-seq_file = sys.argv[3] #Reference library(genome/cDNA)
-nt_spec = sys.argv[4] #only show reactivity for AC or ATCG
-flag_in = sys.argv[5] # perform 2-8% normalization (1) or not (0)
-threshold = sys.argv[6] #Threshold to cap the reactivities
-output_file = sys.argv[7]
-
-
-distri_p = parse_dist(dist_file1)
-distri_m = parse_dist(dist_file2)
-threshold = float(threshold)
-
-
-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+'/' 
-
-h = file(syspath+"react.txt",'w')
-flag_in = int(flag_in)
-
-seqs = SeqIO.parse(open(seq_file),'fasta');
-nt_s = set()
-for i in range(len(nt_spec)):
-    nt_s.add(nt_spec[i])
-
-flag = 0
-trans = []
-distri_p = distri_p[1]
-distri_m = distri_m[1]
-
-#thres = int(threshold)
-
-
-transcripts = {}
-for seq in seqs:
-    n = seq.id
-    trans.append(n)
-    transcripts[n] = seq.seq.tostring()
-    
-
-#print(distri_p)
-        
-
-for i in range(0, len(trans)):
-    h.write(trans[i])
-    h.write('\n')       
-    for j in range(len(distri_p[trans[i]])):
-        distri_p[trans[i]][j] = math.log((int(distri_p[trans[i]][j])+1),math.e)
-    for j in range(len(distri_m[trans[i]])):
-        distri_m[trans[i]][j] = math.log((int(distri_m[trans[i]][j])+1),math.e)       
-    s_p = sum(distri_p[trans[i]])
-    s_m = sum(distri_m[trans[i]])
-    length = len(distri_p[trans[i]])
-    if s_p!= 0 and s_m!= 0:
-        r = []
-        for j in range(0, len(distri_p[trans[i]])):
-            f_p = (float(distri_p[trans[i]][j]))/float(s_p)*length
-            f_m = (float(distri_m[trans[i]][j]))/float(s_m)*length
-            raw_react = f_p-f_m
-            r.append(max(0, raw_react))
-                
-    if s_p!= 0 and s_m!= 0:    
-        for k in range(1,(len(r)-1)):
-            if transcripts[trans[i]][k-1] in nt_s:
-                h.write(str(r[k]))
-                h.write('\t')
-            else:
-                h.write('NA')
-                h.write('\t')
-        k = k+1
-        if transcripts[trans[i]][k-1] in nt_s:
-            h.write(str(r[k]))
-            h.write('\n')
-        else:
-            h.write('NA')
-            h.write('\n')
-            
-
-h.close()
-
-if flag_in:
-    react_norm((syspath+"react.txt"),output_file, threshold)
-else:
-    h_o = file(output_file, 'w')
-    f_i = open(syspath+"react.txt")
-    for aline in f_i.readlines():
-        h_o.write(aline.strip())
-        h_o.write('\n')
-os.system("rm -f "+syspath+"react.txt")
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