# HG changeset patch # User devteam # Date 1416587339 18000 # Node ID 96a82796275011711852a51610ff87a3848e2a38 # Parent d2817a631a7bd8e2f6ff9d77df3501be1ec79f6c Uploaded updated scripts, removed *.pyc and .DS_Store diff -r d2817a631a7b -r 96a827962750 Iterative_mapping/._.DS_Store Binary file Iterative_mapping/._.DS_Store has changed diff -r d2817a631a7b -r 96a827962750 Iterative_mapping/._iterative_map.xml Binary file Iterative_mapping/._iterative_map.xml has changed diff -r d2817a631a7b -r 96a827962750 Iterative_mapping/read_file.pyc Binary file Iterative_mapping/read_file.pyc has changed diff -r d2817a631a7b -r 96a827962750 Iterative_mapping/read_s_file.pyc Binary file Iterative_mapping/read_s_file.pyc has changed diff -r d2817a631a7b -r 96a827962750 get_reads/._.DS_Store Binary file get_reads/._.DS_Store has changed diff -r d2817a631a7b -r 96a827962750 get_reads/read_file.pyc Binary file get_reads/read_file.pyc has changed diff -r d2817a631a7b -r 96a827962750 predict/._.DS_Store Binary file predict/._.DS_Store has changed diff -r d2817a631a7b -r 96a827962750 predict/._predict_RNAs.py Binary file predict/._predict_RNAs.py has changed diff -r d2817a631a7b -r 96a827962750 predict/parse_dis_pac.pyc Binary file predict/parse_dis_pac.pyc has changed diff -r d2817a631a7b -r 96a827962750 predict/predict_RNAs.py --- a/predict/predict_RNAs.py Tue Nov 18 16:24:04 2014 -0500 +++ b/predict/predict_RNAs.py Fri Nov 21 11:28:59 2014 -0500 @@ -1,6 +1,9 @@ #RNA structure prediction & Output and illustrate reactivities import sys +import shlex +import subprocess +import tarfile from parse_dis_pac import * from read_file import * from Bio import SeqIO @@ -15,12 +18,12 @@ output_file = sys.argv[4] -flag = 0 +flag = False 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 + flag = True syspath = os.getcwd() @@ -38,54 +41,55 @@ #predict RNA structures -output_directory = os.path.join(syspath, "output_files/") -os.makedirs(output_directory) +output_directory = os.path.join(syspath, "output_files") +if not os.path.exists(output_directory): + os.makedirs(output_directory) 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"+" "+output_directory+id_s+".ct") - if flag == 1: + fh = file(os.path.join(syspath,"temp.txt"), 'w') + fh.write('>'+id_s) + fh.write('\n') + fh.write(seqs[id_s]) + fh.close() + if not flag: + command = shlex.split('Fold %s %s' % (os.path.join(syspath, temp.txt), os.path.join(output_directory, '%s.ct' % id_s))) + subprocess.call(command) + else: if id_s in react: - f = file(syspath+"constraint.txt",'w') - make_plot(react[id_s],id_s,(output_directory)) #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') + fh = file(os.path.join(syspath, "constraint.txt"), 'w') + make_plot(react[id_s], id_s, output_directory) #make a plot of the distribution of the reactivites of the input RNA 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') + fh.write(str(j+1)) + fh.write('\t') + fh.write(str(react[id_s][j])) + fh.write('\n') #h.write(str(react[id_s][j])) #Output the reactivities #h.write('\t') - f.close() + fh.close() #h.write('\n') #h.write('\n') - os.system("Fold "+syspath+"temp.txt"+" -sh"+" "+syspath+"constraint.txt"+" "+output_directory+id_s+".ct") + command = shlex.split("Fold %s -sh %s %s" % (os.path.join(syspath, "temp.txt"), + os.path.join(syspath, "constraint.txt"), + os.path.join(output_directory, "%s.ct" % id_s))) + subprocess.call(command) else: print(id_s+" not in the data of react!") - os.system("draw "+output_directory+id_s+".ct "+output_directory+"/"+id_s+".ps") + command = shlex.split('draw %s.ct %s.ps' % (os.path.join(output_directory, id_s), os.path.join(output_directory, id_s))) + subprocess.call(command) else: print(id_s+" not in the data of sequences!") #Remove the unnecessary files -os.system("tar -zcvPf "+output_file+" "+output_directory+"/"+"*.* 2>"+output_directory+"log.txt") -os.system("rm -f "+syspath+"temp.txt") -os.system("rm -r "+output_directory) -if flag == 1: - os.system("rm -f "+syspath+"constraint.txt") - # h.close() - - - - - +tarball = tarfile.open(output_file, 'w:gz') +for filename in os.listdir(output_directory): + filepath = os.path.join(output_directory, filename) + print filepath + tarball.add(filepath, arcname=filename) +print os.listdir(syspath) +print os.listdir(output_directory) +# tarball.add('%s.tif' % os.path.join(syspath, id_s), arcname='%s.tif' % id_s) +tarball.close() \ No newline at end of file diff -r d2817a631a7b -r 96a827962750 predict/read_file.pyc Binary file predict/read_file.pyc has changed diff -r d2817a631a7b -r 96a827962750 predict/rtts_plot.py --- a/predict/rtts_plot.py Tue Nov 18 16:24:04 2014 -0500 +++ b/predict/rtts_plot.py Fri Nov 21 11:28:59 2014 -0500 @@ -2,6 +2,7 @@ #Make a plot of reactivity distribution import sys +import os import numpy as np import matplotlib from pylab import * @@ -46,7 +47,7 @@ ax.set_xticklabels(np.arange(0,upmax,intervel*tail)) ax.set_title(id_s+" reactivity distribution") - savefig(path+id_s+'.tif') + savefig(os.path.join(path, id_s+'.tif')) diff -r d2817a631a7b -r 96a827962750 predict/rtts_plot.pyc Binary file predict/rtts_plot.pyc has changed diff -r d2817a631a7b -r 96a827962750 reactivity_cal/parse_dis_react.pyc Binary file reactivity_cal/parse_dis_react.pyc has changed diff -r d2817a631a7b -r 96a827962750 reactivity_cal/react_norm_function.pyc Binary file reactivity_cal/react_norm_function.pyc has changed