Moderator: Jeroen Van Goey
Jeroen Van Goey ♦ 2.2k
- Reputation:
- 2,210
- Status:
- Trusted
- Location:
- Ghent, Belgium
- Website:
- http://jeroen.vangoey.be/
- Twitter:
- @BioGeek
- Last seen:
- 2 years, 5 months ago
- Joined:
- 9 years ago
- Email:
- j*************@gmail.com
Just Another Genome Hacker,
Bioinformatics software developer at Applied Maths
Also known as BioGeek on the web.
Posts by Jeroen Van Goey
<prev
• 60 results •
page 1 of 6 •
next >
10
votes
2
answers
4.9k
views
7 follow
2
answers
... I have the following FASTA file, `original.fasta`:
>foo
GCTCACACATAGTTGATGCAGATGTTGAATTCACTATGAGGTGGGAGGATGTAGGGCCA
I need to change the record id from `foo` to `bar`, so I wrote the following code:
from Bio import SeqIO
original_file = r"path\to\original.fasta"
corr ...
written 3.6 years ago by
Jeroen Van Goey ♦ 2.2k
• updated
22 months ago by
lakshmi.bioinformatics • 20
4
votes
0
answers
1.2k
views
0
answers
... I'm using dbFetch from EBI in a project. I construct URLs from the format
https://www.ebi.ac.uk/Tools/dbfetch/emblfetch?id=[ACCESSION_NUMBER]
to retrieve sequences, e.g.:
https://www.ebi.ac.uk/Tools/dbfetch/emblfetch?id=CO069431
Accession numbers need to be of the format 1 letter + 5 numerals O ...
written 3.8 years ago by
Jeroen Van Goey ♦ 2.2k
• updated
3.7 years ago by
Biostar ♦♦ 20
0
votes
1
answer
1.8k
views
1
answers
... Input names could be changed, so I would prefer a technique that looks at the data itself. However, if that is not possible, looking at the input names might be my only/best bet.
...
written 4.4 years ago by
Jeroen Van Goey ♦ 2.2k
7
votes
1
answer
1.8k
views
1
answer
... When using the SPAdes Genome Assembler, you can use either the BayesHammer read error correction tool for Illumina reads or the IonHammer read error correction tool for IonTorrent data.
I want to use SPAdes in a general workflow and I want to know if there is an automatic way to determine if reads ...
written 4.4 years ago by
Jeroen Van Goey ♦ 2.2k
• updated
4.4 years ago by
arno.guille • 400
17
votes
3
answers
4.0k
views
8 follow
3
answers
... http://anthonyneedsajob.com/
What happened?
Anthony (Biostar user page) will soon start on an adventure in an exciting startup, but starting 1st of October 2013, he has no real source of income.
Since Anthony can not sit on his hands, he is now looking for partners to tackle exciting technical pr ...
written 5.5 years ago by
Jeroen Van Goey ♦ 2.2k
• updated
5.5 years ago by
always_learning • 960
2
votes
3
answers
3.4k
views
3
answers
... r.id in the line `
records = (r for r in SeqIO.parse(input_file, "fasta") if r.id in wanted)
gives back something from the form 'gnl|TC-DB|P0A334'. So, just changing that line to
records = (r for r in SeqIO.parse(input_file, "fasta") if r.id.split('|')[2] in wanted)
will work. I will assume th ...
written 5.9 years ago by
Jeroen Van Goey ♦ 2.2k
3
votes
3
answers
16k
views
3
answers
... Are you following the Entrez Usage Guidlines? Specifically:
For any series of more than 100 requests, do this at weekends or
outside USA peak times. This is up to you to obey.
Make no more than three requests every seconds (relaxed from at most one request every three seconds in early 2009). Thi ...
written 6.1 years ago by
Jeroen Van Goey ♦ 2.2k
0
votes
13
answers
4.2k
views
13
answers
... As far as I know there is no such button, but you can reach the moderators via the mailinglist: biostar-central@googlegroups.com
...
written 6.1 years ago by
Jeroen Van Goey ♦ 2.2k
1
vote
3
answers
8.1k
views
3
answers
... @/Vari: I have sent you an e-mail with some more information.
...
written 6.2 years ago by
Jeroen Van Goey ♦ 2.2k
2
votes
13
answers
4.2k
views
13
answers
... The project that Nikolay Vyahhi metioned that he was working on has gone live in the meantime: rosalind.info is a Project Euler like website with lots of small bioinformatics programming problems. It doesn't have the student/expert matching component though.
...
written 6.2 years ago by
Jeroen Van Goey ♦ 2.2k
Latest awards to Jeroen Van Goey
Great Question
3.5 years ago,
created a question with more than 5,000 views.
For Salary For A Bioinformatics Programmer In Europe?
Appreciated
4.6 years ago,
created a post with more than 5 votes.
For A: Free Hosting For A Bioinformatics Web Application ?
Popular Question
4.9 years ago,
created a question with more than 1,000 views.
For My Friend Anthony Made This Cool Mini-Site To Find A Freelance Bioinformatics Job. Can You Help Him Out?
Good Answer
4.9 years ago,
created an answer that was upvoted at least 5 times.
For A: Free Hosting For A Bioinformatics Web Application ?
Appreciated
5.0 years ago,
created a post with more than 5 votes.
For A: Which Operating System Do You Prefer For Bioinformatics?
Appreciated
5.0 years ago,
created a post with more than 5 votes.
For A: Use Python To List Filename With Specific Extensions.
Appreciated
5.0 years ago,
created a post with more than 5 votes.
For A: Which Bioinformatics Tools Are Written In Python
Good Question
5.0 years ago,
asked a question that was upvoted at least 5 times.
For Salary For A Bioinformatics Programmer In Europe?
Appreciated
5.0 years ago,
created a post with more than 5 votes.
For A: Experiences With Cloud Computing In Bioinformatics
Appreciated
5.0 years ago,
created a post with more than 5 votes.
For A: Provide A Book Review For "Bioinformatics Programming Using Python" By Mitchell
Good Answer
5.0 years ago,
created an answer that was upvoted at least 5 times.
For A: Helping Biostar Grow
Appreciated
5.0 years ago,
created a post with more than 5 votes.
For A: Recommend Your Favorite Bioinformatics Books
Appreciated
5.0 years ago,
created a post with more than 5 votes.
For A: How Far Does Bioinformatics Go?
Appreciated
5.0 years ago,
created a post with more than 5 votes.
For A: Looking For Linux Vendors To Order A Centos/Ubuntu Based Webserver To Host Bioin
Appreciated
5.0 years ago,
created a post with more than 5 votes.
For Provide A Book Review For "Bioinformatics Programming Using Python" By Mitchell L. Model
Appreciated
5.0 years ago,
created a post with more than 5 votes.
For A: Your Favorite Bioinformatics Blogs (March 2010)
Appreciated
5.0 years ago,
created a post with more than 5 votes.
For Salary For A Bioinformatics Programmer In Europe?
Good Answer
5.0 years ago,
created an answer that was upvoted at least 5 times.
For A: Free Hosting For A Bioinformatics Web Application ?
Good Answer
5.0 years ago,
created an answer that was upvoted at least 5 times.
For A: Which Bioinformatics Tools Are Written In Python
Good Answer
5.0 years ago,
created an answer that was upvoted at least 5 times.
For A: Use Python To List Filename With Specific Extensions.
Appreciated
5.0 years ago,
created a post with more than 5 votes.
For A: Can Biopython Parse Gzipped Xml From Blast?
Good Answer
5.0 years ago,
created an answer that was upvoted at least 5 times.
For A: Experiences With Cloud Computing In Bioinformatics
Appreciated
5.0 years ago,
created a post with more than 5 votes.
For A: Free Hosting For A Bioinformatics Web Application ?
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1812 users visited in the last hour