Moderator: Joe
Joe ♦ 16k
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- Joined:
- 4 years, 5 months ago
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Recently finished my PhD, so now I pretend to know what I’m talking about on Bioinformatics forums...
Posts by Joe
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... Do you actually need alignment for this, or are the matches (reasonably) well conserved? Fuzzy matching, as already mentioned, or a regex approach might be sufficient? ...
written 2 hours ago by
Joe ♦ 16k
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... You are moving the goalposts now, getting the indexes of all the different positions is the output you requested, so that's the code I wrote.
If you need a specific form of output, you need to be explicit about this in your question. You also haven't shown what you've tried on this front.
You can ...
written 2 hours ago by
Joe ♦ 16k
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... I think you're underestimating the role of the thesis in the UK PhD process. Every UK PhD absolutely is judged on their making of a contribution to science, but to suggest papers are the only way to do that isn't accurate in my view. ...
written 3 hours ago by
Joe ♦ 16k
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... That should be easy enough. I'd suggest unrolling the list comprehension in to a proper loop structure, and then you just add a few `if` statements to ensure the character in question is not `X` or `-`.
You could edit the list comp, but it starts to get unwieldy after a while. Off the top of my hea ...
written 4 hours ago by
Joe ♦ 16k
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... What do you want to do if the consensus has an ambiguous character?
Otherwise you just need to loop over the sequences in the alignment:
from Bio import AlignIO
from Bio.Align import AlignInfo # To generate a trivial 'dumb' consensus
aln = AlignIO.read(file, format)
summary = Alig ...
written 7 hours ago by
Joe ♦ 16k
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... 2 things:
1. If your question fits in a single sentence, you almost certainly have not provided enough information. What you've already tried and how/why it didn't work is a good start.
2. This is not a `Forum` type post, so I've changed it, but please bear in mind for the future. ...
written 16 hours ago by
Joe ♦ 16k
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... Yep - its a very backwards system. Your analogy is not quite right, as the expectation is not that the researcher themselves pay.
It is most certainly a con that we have to pay to publish and pay to access oftentimes. ...
written 16 hours ago by
Joe ♦ 16k
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... I'd add to this that in the UK, its actually pretty unusual to get papers during the PhD as they're only about 3 years long, particularly in experimental biology. It's a bit more normal in chemistry and physics. It's certainly something academics will push for, as long as it adds to, and not distrac ...
written 16 hours ago by
Joe ♦ 16k
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... Welcome to the broken world of academic publishing.
For the record, there are lots of journals that support open-access science (not that this always means you don't have to pay, just that you don't pay to access).
Typically, you're going to be looking at online journals since they aren't passing ...
written 17 hours ago by
Joe ♦ 16k
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... Those numbers should correspond to the indexes you are interested in, exactly what is the problem?
If you want to generalise this for the full alignment you can do:
from Bio import AlignIO
aln = AlignIO.parse(..., ...)
for i in range(aln.get_alignment_length()):
if len(se ...
written 1 day ago by
Joe ♦ 16k
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