Moderator: Joe

gravatar for Joe
Joe17k
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16,690
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Location:
United Kingdom
Website:
http://www2.warwick.ac...
Twitter:
JRJHealey
Last seen:
13 hours ago
Joined:
4 years, 9 months ago
Email:
j*********@gmail.com

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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Comment: C: Motif search on a DNA sequence in a gff file (ipdSummary output)
... 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 Joe17k
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Answer: A: Motif search on a DNA sequence in a gff file (ipdSummary output)
... 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 Joe17k
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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 Joe17k
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Comment: C: BioPython write combined nexus files
... 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 Joe17k
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Comment: C: BioPython write combined nexus files
... 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 Joe17k
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Answer: A: BioPython write combined nexus files
... 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 Joe17k
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Comment: C: BioPython write combined nexus files
... 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 Joe17k
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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 Joe17k
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Comment: C: What technique does proteomic software use to predict if separate sequences orig
... 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 Joe17k
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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 Joe17k

Latest awards to Joe

Appreciated 17 hours ago, created a post with more than 5 votes. For C: is fortran still used in bioinformatics?
Teacher 22 hours ago, created an answer with at least 3 up-votes. For A: Run a Python program in Ubuntu
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Merging gff/gbk to create a 'full' gbk
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Merging gff/gbk to create a 'full' gbk
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Run a Python program in Ubuntu
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Merging gff/gbk to create a 'full' gbk
Scholar 3 months ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Scholar 3 months ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Run a Python program in Ubuntu
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Run a Python program in Ubuntu
Appreciated 4 months ago, created a post with more than 5 votes. For C: is fortran still used in bioinformatics?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Run a Python program in Ubuntu
Popular Question 4 months ago, created a question with more than 1,000 views. For Merging gff/gbk to create a 'full' gbk
Popular Question 4 months ago, created a question with more than 1,000 views. For Merging gff/gbk to create a 'full' gbk
Scholar 5 months ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Scholar 5 months ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Run a Python program in Ubuntu
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: fasta seq header
Scholar 5 months ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Scholar 5 months ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Run a Python program in Ubuntu
Popular Question 6 months ago, created a question with more than 1,000 views. For Merging gff/gbk to create a 'full' gbk
Appreciated 6 months ago, created a post with more than 5 votes. For C: is fortran still used in bioinformatics?
Popular Question 6 months ago, created a question with more than 1,000 views. For Merging gff/gbk to create a 'full' gbk
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: cuda-accelerated sequence alignment program

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