User: cschu181

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Posts by cschu181

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Comment: C: from protein to tRNA combinations
... Maybe it's an extra level of complexity in the task (or a misunderstanding). ...
written 29 days ago by cschu1812.5k
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Comment: C: from protein to tRNA combinations
... Ouch, of course, it should be `*`, good spot, thanks! Just, fyi `codon_table.get(aa, 0)` returns `0` if `aa` is not in the table instead of erroring out. Re your other suggestions -- yea, second those! Except if we have an `M`-polymer or `W`-polymer with length < 5001 :) ...
written 29 days ago by cschu1812.5k
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Comment: C: from protein to tRNA combinations
... What's the error you're getting? I'd do something like this: codon_table = {"M": ["AUG"], "P": ["CCA", "CCC", "CCG", "CCU"], ...} for record in protein: n_combinations = 0 for aa in record.seq: n_combinations *= codon_table.get(aa, 0) if n_combinati ...
written 29 days ago by cschu1812.5k
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Comment: C: from protein to tRNA combinations
... > I'm really thankful, and sorry to pull this, I know It's probably lame, I just thought i could find some help if i can No worries, I just asked for the purpose of understanding how to better help you with this. Have a look at _r_am's answer below (even if it is struck through). Build yoursel ...
written 4 weeks ago by cschu1812.5k
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Comment: C: from protein to tRNA combinations
... The bottom six lines don't look correctly indented. What Asaf was trying to tell you: in Python the indentation of code blocks is an essential part of the control flow. If you don't indent correctly, the code might work but would potentially do wrong things. In other programming languages this is ...
written 4 weeks ago by cschu1812.5k
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Comment: C: from protein to tRNA combinations
... > a protein sequence that needs all possible combinations of tRNAs that it can be converted to I assume you mean codons (or anticodons) instead of tRNAs? Concerning your code: I'm sorry, but it doesn't seem to make sense. Can you explain what your approach to the problem is and what you think y ...
written 4 weeks ago by cschu1812.5k
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Comment: C: Mutation Rate in Python
... In your loop: row = list(map(int, row)) print(1 - max(row) / sum(row)) Edit: Note: the text (esp. the code) of the question appears to have changed since the initial posting, so this comment doesn't seem to make sense any more. ...
written 11 weeks ago by cschu1812.5k
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Comment: C: Setting up BUSCO well
... https://gitlab.com/ezlab/busco/-/issues/342 ...
written 12 weeks ago by cschu1812.5k
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Comment: C: Read DNA sequence from FASTA rising a subclass?
... Indeed, instead of the `return False` you'd `raise BadSequenceException(x + " is not a valid nucleobase")` (or something like that). In addition to that, do you really want to add the empty sequence (upon encountering the first sequence header `>`) to the set of sequences? ...
written 12 weeks ago by cschu1812.5k
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Comment: C: Setting up BUSCO well
... OP needs to be careful, though, what a successful testrun means. With a previous BUSCO version, I once had the .odb databases unreachable due to filesystem permissions. Did that stop BUSCO from running? No, it just ran everything against the integrated mouse (I think it was mouse) database. It repor ...
written 12 weeks ago by cschu1812.5k

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Appreciated 4 months ago, created a post with more than 5 votes. For A: Getting PFAM database
Scholar 5 months ago, created an answer that has been accepted. For A: Simple python script to convert ambiguity codes
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