【Rosalind】Finding a Protein Motif – 正则表达式的使用

最新推荐文章于 2022-11-20 23:52:11 发布

EmmettPeng

最新推荐文章于 2022-11-20 23:52:11 发布

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分类专栏： Rosalind 文章标签： python 正则表达式生物信息学

本文链接：https://blog.youkuaiyun.com/Emmett_Bioinfo/article/details/109274743

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Rosalind习题Finding a Protein Motif

先祝大家中秋和国庆双节快乐！
在这个日历我还在努力地学习代码（指只有晚上写了2h白天都在睡觉）zzzz
最近在做Rosalind上的这道习题，其中用到了Python中的正则表达式，也就是调用了re模块。之前在学perl（没有学会的那种学）的时候接触过正则表达式，但是自己用的并不是很多，这次正好找到个机会使用一下，还不是很熟练。

Problem

To allow for the presence of its varying forms, a protein motif is represented by a shorthand as follows: [XY] means “either X or Y” and {X} means “any amino acid except X.” For example, the N-glycosylation motif is written as N{P}[ST]{P}.

You can see the complete description and features of a particular protein by its access ID “uniprot_id” in the UniProt database, by inserting the ID number into

http://www.uniprot.org/uniprot/uniprot_id

Alternatively, you can obtain a protein sequence in FASTA format by following

http://www.uniprot.org/uniprot/uniprot_id.fasta

For example, the data for protein B5ZC00 can be found at http://www.uniprot.org/uniprot/B5ZC00.

Given: At most 15 UniProt Protein Database access IDs.

Return: For each protein possessing the N-glycosylation motif, output its given access ID followed by a list of locations in the protein string where the motif can be found.

Sample Dataset
A2Z669
B5ZC00
P07204_TRBM_HUMAN
P20840_SAG1_YEAST
Sample Output
B5ZC00
85 118 142 306 395
P07204_TRBM_HUMAN
47 115 116 382 409
P20840_SAG1_YEAST
79 109 135 248 306 348 364 402 485 501 614<