Moderator: Joe
Joe ♦ 17k
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- Website:
- http://www2.warwick.ac...
- Twitter:
- JRJHealey
- Last seen:
- 13 hours ago
- Joined:
- 4 years, 9 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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... Please do, just be aware that designing robust regexes is a bit of a dark art, so scrutinise your output data very carefully, since I know that RegEx is not as optimal as it perhaps could be.
If the answer solves your question, don't forget to toggle it as Accepted, by the way. ...
written 17 hours ago by
Joe ♦ 17k
3
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... This was a pretty fun one, if a little messy.
Try this:
#!/usr/bin/env python
import sys
import re
from itertools import chain
# This is not strictly necessary, but helps break the regex up over multiple lines
# so it's a bit easier to read:
a___a = "((\*\*)?A ...
written 18 hours ago by
Joe ♦ 17k
5
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2
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Answer:
A: What is an OTU?
... In addition to the technical definition above, a more 'conceptual' definition is that an OTU is just a way of saying:
*"This cluster of things is the same, and different from that cluster of things*"
**without** having to assign a more 'meaningful' moniker to it (like a specific species name etc ...
written 1 day ago by
Joe ♦ 17k
0
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... If this is a genuine bug, it must have come in in the subsequent releases. You could try either downgrading your biopython to `1.74` and give that a go, or post a bug report at the `biopython` github issues page (they have a template for providing all the necessary information).
I'm afraid I'm out ...
written 1 day ago by
Joe ♦ 17k
0
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2
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... No, that's not a code line, it's just the printed output of the previous command showing a description of the Nexus object.
Do you have all the necessary permissions to create and modify files in the directory you're working in?
Have you tried their example files? Perhaps there's some issue combin ...
written 3 days ago by
Joe ♦ 17k
0
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... Can you specify what versions of `python` and `biopython` you are using?
I've just attempted to run the documented examples, with their example files as at: https://biopython.org/wiki/Concatenate_nexus
It works fine for me on `Python 3.7.3` and `BioPython 1.74`:
**Downloading test data:**
----- ...
written 4 days ago by
Joe ♦ 17k
0
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2
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... I've not used this bit of the module before, but if I had to guess, I'd say the documentation is probably just out of date relative to the codebase.
Looking at https://biopython.org/DIST/docs/api/Bio.Nexus.Nexus-pysrc.html#Nexus.write_nexus_data
There appears to be a 'append' flag to that method, ...
written 5 days ago by
Joe ♦ 17k
1
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Comment:
C: protein and sequence
... Then try GenBank instead, but the process is basically the same. ...
written 5 days ago by
Joe ♦ 17k
0
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... I assume you're talking about mapping peptides?
They are simply mapped back to a known set of reference proteins. If they are sufficiently long, they will map uniquely (assuming that sequence only occurs once in the reference set). Shorter or ambiguity containing sequences might hit multiple refere ...
written 7 days ago by
Joe ♦ 17k
0
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1
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1
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Comment:
C: Database from .gbk files
... No worries - sorry we can't be more directly useful. It's a pretty niche tool so you're just going to have to keep experimenting I think. ...
written 7 days ago by
Joe ♦ 17k
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For C: is fortran still used in bioinformatics?
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For Merging gff/gbk to create a 'full' gbk
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For A: Run a Python program in Ubuntu
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For A: Script/Application to create a genbank format sub-sequence
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5 months ago,
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For A: Script/Application to create a genbank format sub-sequence
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For A: Run a Python program in Ubuntu
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For C: cuda-accelerated sequence alignment program
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