Databases parser for ENSEMBL and UNIPROT

[dsmutin]

Done homework for API request parsing

[rinnifox]

Hi Daniil!

Comments regarding your homework:

1. ENSEMBL. Your expression ENS.*{11} is incorrect in terms of syntax. It is impossible to use {11} after *, this item is not quantifiable. Also, I recommend you checking this page to get the idea of how ENSEMBL IDs should be constructed, which characters and how many should be there.
2. Uniprot. In yor expression r'\w{6} you denote any 6 non-word symbols. It does not match any of symbols in Uniprot example IDs. Moreover, in the lecture materials I provided a link for Uniprot accession ID construction rules as the actual expression for this database is rather complex, and it is explicitly indicated in the home task file that you should use this materials to complete a correct expression for Uniprot.
3. Your code is running with errors. In re.search you provide a pattern in figure brackets, which leads to an error. Have you tried running the code yourself?

Fix this please before the next lecture, ok?

[dsmutin]

Thank you for comments, fixed

[rinnifox]

Currently, your expression for Uniprot [A-Z]\w{5}|\w{7}|\w{9} allows three options:

1. One [A-Z] symbol then 5 other word characters ([a-zA-Z0-9_]);
2. 7 word characters ([a-zA-Z0-9_]) - please note that here you don't have the first [A-Z] symbol (it is not included in your alternative expressions);
3. 9 word characters ([a-zA-Z0-9_]) - here you don't have first [A-Z] symbol as well.

Since you do not have a linkage to the end of the sequence, almost any string will match in case it has first 6, 7 or 9 symbols matching the indicated patterns.
So you have to link the pattern to the beginning and end of the string, and I also recommend setting it up more precisely accounting for different options in the beginning ([OPQ] or [A-N,R-Z]).

For ENSEMBL, ENS[A-Z]{0,3}|MGP_[a-zA-Z]*_)\w\w?\d{11} seems to be almost correct but note please that currently you have [A-Z]{0,3} for species but you are not accounting for feature prefixes, check this also please.

[dsmutin]

I believe that it finally works, thank you for all responses!
All fixed

[rinnifox]

Seems to be correct now! You can merge it to main.