imported>Minsukim |
imported>Minsukim |
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| | <h2> </h2> | | <h2> </h2> |
| | | | |
| − | <h2>function</h2>
| + | <p><a href="http://biolecture.org/index.php?title=Minsu_Kim/python /Basics">Python basics</a></p> |
| − | | |
| − | <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 />
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| − | 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 = f.readline()<br /> | |
| − | f.close</p>
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| − | | |
| − | <p>text = list(a)</p>
| |
| − | | |
| − | <p>for i in range(0,len(text)):<br />
| |
| − | if text[i] == 'T':<br />
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| − | text[i] = 'U'<br />
| |
| − | a = ''.join(text)</p>
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| − | | |
| − | <p>print(a)</p>
| |
| − | | |
| − | <p>f = open('rosalind_revc2.txt','r')<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 />
| |
| − | 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 />
| |
| − | 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:400px" /><br />
| |
| − | 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> </p> |
| | | | |
| − | <p> </p> | + | <p><a href="http://biolecture.org/index.php?title=Minsu_Kim/python/Rosalind">Rosalind</a></p> |
