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Minsu Kim/python/Rosalind

4,066 bytes added, 18:27, 12 December 2017
Created page with "<h2>function</h2> <p>def patterncount(text, pattern):<br />     count=0<br />     for i in range(0,len(text)):<br />         if(text[i:le..."
<h2>function</h2>

<p>def patterncount(text, pattern):<br />
&nbsp; &nbsp; count=0<br />
&nbsp; &nbsp; for i in range(0,len(text)):<br />
&nbsp; &nbsp; &nbsp; &nbsp; if(text[i:len(pattern)+i]==pattern):<br />
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; count += 1<br />
&nbsp; &nbsp; return count</p>

<p>def complementing(sequence):<br />
&nbsp; &nbsp; sequence = sequence[::-1]<br />
&nbsp; &nbsp; text = list(sequence)<br />
&nbsp; &nbsp; for i in range(0,len(text)):<br />
&nbsp; &nbsp; &nbsp; &nbsp; if text[i] == &#39;A&#39;:<br />
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; text[i] = &#39;T&#39;<br />
&nbsp; &nbsp; &nbsp; &nbsp; elif text[i] == &#39;G&#39;:<br />
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; text[i] = &#39;C&#39;<br />
&nbsp; &nbsp; &nbsp; &nbsp; elif text[i] == &#39;C&#39;:<br />
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; text[i] = &#39;G&#39;<br />
&nbsp; &nbsp; &nbsp; &nbsp; elif text[i] == &#39;T&#39;:<br />
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; text[i] = &#39;A&#39;<br />
&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;<br />
&nbsp; &nbsp; s = &#39;&#39;.join(text)<br />
&nbsp; &nbsp; print(s)<br />
&nbsp; &nbsp; return 0</p>

<h1>rosalind transcript basic</h1>

<p>f = open(&#39;rosalind_rna.txt&#39;)<br />
a = f.readline()<br />
f.close</p>

<p>text = list(a)</p>

<p>for i in range(0,len(text)):<br />
&nbsp; &nbsp; if text[i] == &#39;T&#39;:<br />
&nbsp; &nbsp; &nbsp; &nbsp; text[i] = &#39;U&#39;<br />
a = &#39;&#39;.join(text)</p>

<p>print(a)</p>

<p>f = open(&#39;rosalind_revc2.txt&#39;,&#39;r&#39;)<br />
b = f.readline()<br />
f.close</p>

<p>b = b[::-1]<br />
text = list(b)</p>

<p>for i in range(0,len(text)):<br />
&nbsp; &nbsp; if text[i] == &#39;A&#39;:<br />
&nbsp; &nbsp; &nbsp; &nbsp; text[i] = &#39;T&#39;<br />
&nbsp; &nbsp; elif text[i] == &#39;G&#39;:<br />
&nbsp; &nbsp; &nbsp; &nbsp; text[i] = &#39;C&#39;<br />
&nbsp; &nbsp; elif text[i] == &#39;C&#39;:<br />
&nbsp; &nbsp; &nbsp; &nbsp; text[i] = &#39;G&#39;<br />
&nbsp; &nbsp; elif text[i] == &#39;T&#39;:<br />
&nbsp; &nbsp; &nbsp; &nbsp; text[i] = &#39;A&#39;<br />
&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;<br />
b = &#39;&#39;.join(text)</p>

<p>print(b)</p>

<h2>Computing CG Content</h2>

<p>f_fa = 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_fa.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>
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