View source for Minsu Kim/python/Rosalind

<h4>I solve the problem related&nbsp;to the bioinformatics in web site : rosalind</h4>

<h1>Problem</h1>

<p>basic problem</p>

<p><a href="http://biolecture.org/index.php?title=Minsu_Kim/python/Rosalind / b1">[1]</a>&nbsp;&nbsp; <a href="http://biolecture.org/index.php?title=Minsu_Kim/python/Rosalind / b2">[2]</a>&nbsp; &nbsp;<a href="http://biolecture.org/index.php?title=Minsu_Kim/python/Rosalind / b3">[3]</a></p>

<p>related with bioinformatics</p>

<p><a href="http://biolecture.org/index.php?title=Minsu_Kim/python/Rosalind / problem1">[1]</a>&nbsp; &nbsp;<a href="http://biolecture.org/index.php?title=Minsu_Kim/python/Rosalind / problem2">[2]</a>&nbsp; &nbsp;<a href="http://biolecture.org/index.php?title=Minsu_Kim/python/Rosalind / problem3">[3]</a>&nbsp; &nbsp;<a href="http://biolecture.org/index.php?title=Minsu_Kim/python/Rosalind /problem4">[4]</a> &nbsp; <a href="http://biolecture.org/index.php?title=Minsu_Kim/python/Rosalind /problem5">[5]</a> &nbsp; <a href="http://biolecture.org/index.php?title=Minsu_Kim/python/Rosalind /problem6">[6]</a></p>

<p><a href="http://biolecture.org/index.php?title=Minsu_Kim/python/Rosalind / problem7">[7]</a> &nbsp; <a href="http://biolecture.org/index.php?title=Minsu_Kim/python/Rosalind / problem8">[8]</a> &nbsp; <a href="http://biolecture.org/index.php?title=Minsu_Kim/python/Rosalind / problem9">[9]</a> &nbsp; <a href="http://biolecture.org/index.php?title=Minsu_Kim/python/Rosalind / problem10">[10]</a> &nbsp; <a href="http://biolecture.org/index.php?title=Minsu_Kim/python/Rosalind / problem11">[11]</a> &nbsp; <a href="http://biolecture.org/index.php?title=Minsu_Kim/python/Rosalind / problem12">[12]</a></p>

<h2>Computing CG Content</h2>

<p>f&nbsp;= open(&#39;rosalind_gc.txt&#39;,&#39;r&#39;)<br />
seq_list = dict()<br />
for line in f_fa:<br />
&nbsp; &nbsp; if line.startswith(&#39;&gt;&#39;):<br />
&nbsp; &nbsp; &nbsp; &nbsp; name = line.strip(&#39;&gt;&#39;).strip()<br />
&nbsp; &nbsp; &nbsp; &nbsp; seq_list[name] = &#39;&#39;<br />
&nbsp; &nbsp; else:<br />
&nbsp; &nbsp; &nbsp; &nbsp; seq_list[name]= line.strip()<br />
f.close()</p>

<p>seq_CG = dict()<br />
for k in seq_list:<br />
&nbsp; &nbsp; count = 0<br />
&nbsp; &nbsp; s = seq_list[k]<br />
&nbsp; &nbsp; s = list(s)<br />
&nbsp; &nbsp; for i in range(0,len(s)):<br />
&nbsp; &nbsp; &nbsp; &nbsp; if s[i] == &#39;C&#39; or s[i] == &#39;G&#39;:<br />
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; count = count + 1<br />
&nbsp; &nbsp; p = count / len(s)<br />
&nbsp; &nbsp; seq_CG[k] = p</p>

<p>inverse = [(value, key) for key, value in seq_CG.items()]<br />
max(inverse)</p>

<p>import matplotlib.pyplot as plt</p>

<p>seq_list = []<br />
f_fa = open(&#39;Ecoli_genome.fasta&#39;, &#39;r&#39;)<br />
for line in f_fa:<img alt="" src="/ckfinder/userfiles/images/e_coli%20gc%20content.jpg" style="float:right" /><br />
&nbsp; &nbsp; if not line.startswith(&#39;&gt;&#39;):<br />
&nbsp; &nbsp; &nbsp; &nbsp; seq_list.append(line.strip())<br />
tmp_seq = &#39;&#39;.join(seq_list)</p>

<p>count_G = 0<br />
count_C = 0<br />
count_list = []<br />
for tmp_n in tmp_seq:<br />
&nbsp; &nbsp; if tmp_n == &#39;G&#39;:<br />
&nbsp; &nbsp; &nbsp; &nbsp; count_G += 1<br />
&nbsp; &nbsp; if tmp_n == &#39;C&#39;:<br />
&nbsp; &nbsp; &nbsp; &nbsp; count_C += 1<br />
&nbsp; &nbsp; count_list.append(count_G-count_C)</p>

<p>pos_list = range(0,len(tmp_seq))</p>

<p>fig = plt.figure(figsize = (10,6))<br />
ax1 = fig.add_subplot(1,1,1)<br />
ax1.plot(pos_list, count_list, &#39;b-&#39;)<br />
ax1.grid()<br />
plt.show()<br />
f_fa.close()</p>

<p>&nbsp;</p>

<h2>Dynamic Program</h2>

<p>def maxvalue(a,b,c):<br />
&nbsp; &nbsp; a=a+5<br />
&nbsp; &nbsp; b=b-6<br />
&nbsp; &nbsp; c=c-6<br />
&nbsp; &nbsp; return max(a,b,c)<br />
def maxvalue2(a,b,c):<br />
&nbsp; &nbsp; a=a-2<br />
&nbsp; &nbsp; b=b-6<br />
&nbsp; &nbsp; c=c-6<br />
&nbsp; &nbsp; return max(a,b,c)</p>

<p>def compare(a,b):<br />
&nbsp; &nbsp; import numpy as np<br />
&nbsp; &nbsp; scoring = np.zeros([len(a)+1,len(b)+1])<br />
&nbsp; &nbsp; for i in range(0,len(a)+1):<br />
&nbsp; &nbsp; &nbsp; &nbsp; scoring[i,0]=-6*i<br />
&nbsp; &nbsp; for j in range(0,len(b)+1):<br />
&nbsp; &nbsp; &nbsp; &nbsp; scoring[0,j]=-6*j</p>

<p>&nbsp; &nbsp; for row in range(1,len(a)+1):<br />
&nbsp; &nbsp; &nbsp; &nbsp; for column in range(1,len(b)+1):<br />
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; if b[column-1]==a[row-1]:<br />
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; scoring[row,column] = maxvalue(scoring[row-1,column-1],scoring[row-1,column],scoring[row,column-1])<br />
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; if b[column-1]!=a[row-1]:<br />
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; scoring[row,column] = maxvalue2(scoring[row-1,column-1],scoring[row-1,column],scoring[row,column-1])<br />
&nbsp; &nbsp; print(scoring)</p>

<p>&nbsp; &nbsp; list=[]<br />
&nbsp; &nbsp; for row in range(1,len(a)+1):<br />
&nbsp; &nbsp; &nbsp; &nbsp; for column in range(1,len(b)+1):<br />
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; new=scoring[row,column]<br />
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; list.append(new)<br />
&nbsp; &nbsp; mxv=max(list)<br />
&nbsp; &nbsp; print(mxv)</p>

<p><img alt="" src="/ckfinder/userfiles/images/bandicam%202017-12-12%2019-14-32-803.jpg" style="height:530px; width:640px" /></p>