<h2> </h2>
<h2>function</h2> <p>def patterncount(text, pattern):<br /> count=0<br /> for i in range(0,len(text)):<br /> if(text[i:len(pattern)+i]==pattern):<br /> count += 1<br /> return count</p> <p>
def complementing(sequence):<br /> sequence = sequence[::-1]<br /> text = list(sequence)<br /> for i in range(0,len(text)):<br /> if text[i] == 'A':<br /> text[i] = 'T'<
br /> elif text[i] == 'G':<br /> text[i] = 'C'<br /> elif text[i] == 'C':<br /> text[i] = 'G'<br /> elif text[i] == 'T':<br /> text[i] = 'A'<br /> <br /> s = ''.join(text)<br /> print(s)<br /> return 0</p> <h1>rosalind transcript basic</h1> <p>f = open('rosalind_rna.txt')<br />a
href=
f.readline()<br />f.close</p> <p>text = list(a)</p> <p>for i in range(0,len(text)):<br /> if text[i] == 'T'"http:
<br /
> text[i] = 'U'<br /
>a = ''biolecture.
join(text)<org/
p> <p>print(a)</p> <p>f = open('rosalind_revc2.txt','r')<br />b = findex.
readline()<br />f.close</p> <p>b = b[::-1]<br />text = list(b)</p> <p>for i in range(0,len(text)):<br /> if text[i] == 'A':<br /> text[i] = 'T'<br /> elif text[i] =php?title=
'G':<br Minsu_Kim/
> text[i] = 'C'<br python /
> elif text[i] == 'C':<br /> text[i] = 'G'<br /> elif text[i] == 'T':<br /> text[i] = 'A'<br /> <br />b = ''.join(text)</p> <p>print(b)</p> <h2>Computing CG Content</h2> <p>f_fa = open('rosalind_gc.txt','r')<br />seq_list = dict()<br />for line in f_fa:<br /> if line.startswith('>'):<br /> name = line.strip('>').strip()<br /> seq_list[name] = ''<br /> else:<br /> seq_list[name]= line.strip()<br />f_fa.close()</p> <p>seq_CG = dict()<br />for k in seq_list:<br /> count = 0<br /> s = seq_list[k]<br /> s = list(s)<br /> for i in range(0,len(s)):<br /> if s[i] == 'C' or s[i] == 'G':<br /> count = count + 1<br /> p = count / len(s)<br /> 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('Ecoli_genome.fasta', 'r')<br />for line in f_fa:<img alt="" src="/ckfinder/userfiles/images/e_coli%20gc%20content.jpg" style="float:right; height:400px; width:400pxBasics"
/>
Python basics<
br /
a>
if not line.startswith('>'):<br /> seq_list.append(line.strip())<br />tmp_seq = ''.join(seq_list)</p> <p>count_G = 0<br />count_C = 0<br />count_list = []<br />for tmp_n in tmp_seq:<br /> if tmp_n == 'G':<br /> count_G += 1<br /> if tmp_n == 'C':<br /> count_C += 1<br /> 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, 'b-')<br />ax1.grid()<br />plt.show()<br />f_fa.close()</p>
<p> </p>
<p> <a href="http://biolecture.org/index.php?title=Minsu_Kim/python/Rosalind">Rosalind</a></p>
