Moderator: Alex Reynolds
Alex Reynolds ♦ 21k
- Reputation:
- 20,810
- Status:
- Trusted
- Location:
- Seattle, WA USA
- Website:
- http://dropbit.com/
- Twitter:
- AlexReynolds
- Scholar ID:
- Google Scholar Page
- Last seen:
- an hour ago
- Joined:
- 7 years, 10 months ago
- Email:
- a************@gmail.com
One of the developers behind the fast BEDOPS suite, whose pug Zac is the bestest pug in the world.
Posts by Alex Reynolds
<prev
• 1,790 results •
page 1 of 179 •
next >
1
vote
2
answers
151
views
2
answers
... The formats of these files are different than what you posted originally.
To answer your question based off of *these* inputs, you could convert the first file to sorted BED via:
$ cut -f2 first.txt | awk -v OFS="\t" -F'[:-]' '{ print $1, $2, $3; }' | sort-bed - > first.bed
Convert the sec ...
written 1 day ago by
Alex Reynolds ♦ 21k
0
votes
2
answers
151
views
2
answers
... And you're missing a column, somewhere, compared with what was in your original question. Which is the correct input? This one, or the input in your question? ...
written 1 day ago by
Alex Reynolds ♦ 21k
0
votes
2
answers
151
views
2
answers
... You have to get rid of that header. Please see my modified answer for stripping the header with `tail -n+2`. ...
written 1 day ago by
Alex Reynolds ♦ 21k
1
vote
2
answers
105
views
2
answers
Answer:
A: Tools to create workflows
... [GNU make][1] is found everywhere and will probably have the fewest limitations and dependencies.
[1]: https://www.gnu.org/software/make/ ...
written 1 day ago by
Alex Reynolds ♦ 21k
0
votes
2
answers
151
views
2
answers
... What does:
$ awk -v OFS="\t" '{ print $1, $4, $5, $2, $3, $6, $7; }' second.txt | head
look like? ...
written 2 days ago by
Alex Reynolds ♦ 21k
2
votes
4
answers
282
views
4
answers
... One way to do this may be to attempt (`try`) to parse on the pipe character, and then just print out the header and sequence as-is if there is no split:
#!/usr/bin/env python
import sys
original_fn = sys.argv[1]
company_fn = sys.argv[2]
map = {}
with open(original_fn, "r ...
written 2 days ago by
Alex Reynolds ♦ 21k
0
votes
4
answers
282
views
4
answers
... Are these the "company" headers or your "original" headers? It would help to see examples of both. You can use the `try..except` block to deal with cases like these, but we'd need to see both types of headers to figure out how to parse both varieties. ...
written 2 days ago by
Alex Reynolds ♦ 21k
0
votes
2
answers
151
views
2
answers
... Convert the first file to a **sorted** BED file:
$ tail -n+2 first.txt | cut -f2 | awk -v OFS="\t" -F'[:-]' '{ print $1, $2, $3; }' | sort-bed - > first.bed
Convert the second file to a sorted BED file:
$ tail -n+2 second.txt | awk -v OFS="\t" '{ print $1, $4, $5, $2, $3, $6, $7; }' ...
written 2 days ago by
Alex Reynolds ♦ 21k
• updated
1 day ago by
genomax ♦ 34k
0
votes
4
answers
282
views
4
answers
... I think that suffix would not throw the exception you reported in your comment above. Can you run the code with the addition of the `try..except` code block I posted above? That should highlight the line that fails to split on the pipe character. ...
written 2 days ago by
Alex Reynolds ♦ 21k
0
votes
1
answer
160
views
1
answers
... It looks like you asked that question, too. The options specified are different, the reference genomes are different and so the inputs are different, and the two answers use different ranges. I would say you should review the links to documentation to understand the options, and review the inputs to ...
written 3 days ago by
Alex Reynolds ♦ 21k
Latest awards to Alex Reynolds
Scholar
1 day ago,
created an answer that has been accepted.
For A: Checking the quality and reliability in bioinformatics
Scholar
2 days ago,
created an answer that has been accepted.
For A: Checking the quality and reliability in bioinformatics
Scholar
2 days ago,
created an answer that has been accepted.
For A: Checking the quality and reliability in bioinformatics
Scholar
3 days ago,
created an answer that has been accepted.
For A: Checking the quality and reliability in bioinformatics
Scholar
7 days ago,
created an answer that has been accepted.
For A: Checking the quality and reliability in bioinformatics
Scholar
8 days ago,
created an answer that has been accepted.
For A: Checking the quality and reliability in bioinformatics
Appreciated
8 days ago,
created a post with more than 5 votes.
For samtools idxstats on indexed BAM failed
Popular Question
10 days ago,
created a question with more than 1,000 views.
For Bedops V2.4 Released
Scholar
17 days ago,
created an answer that has been accepted.
For A: Do these warning messages during my bedops install mean bedops won't work proper
Teacher
17 days ago,
created an answer with at least 3 up-votes.
For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Scholar
17 days ago,
created an answer that has been accepted.
For A: Do these warning messages during my bedops install mean bedops won't work proper
Teacher
17 days ago,
created an answer with at least 3 up-votes.
For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Scholar
18 days ago,
created an answer that has been accepted.
For A: Do these warning messages during my bedops install mean bedops won't work proper
Teacher
18 days ago,
created an answer with at least 3 up-votes.
For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Scholar
19 days ago,
created an answer that has been accepted.
For A: Do these warning messages during my bedops install mean bedops won't work proper
Teacher
19 days ago,
created an answer with at least 3 up-votes.
For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Scholar
19 days ago,
created an answer that has been accepted.
For A: Do these warning messages during my bedops install mean bedops won't work proper
Scholar
20 days ago,
created an answer that has been accepted.
For A: Do these warning messages during my bedops install mean bedops won't work proper
Scholar
20 days ago,
created an answer that has been accepted.
For A: No PhyloP score for first stretch of chromosome?
Teacher
23 days ago,
created an answer with at least 3 up-votes.
For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Teacher
24 days ago,
created an answer with at least 3 up-votes.
For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Teacher
24 days ago,
created an answer with at least 3 up-votes.
For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Scholar
24 days ago,
created an answer that has been accepted.
For A: Do these warning messages during my bedops install mean bedops won't work proper
Teacher
28 days ago,
created an answer with at least 3 up-votes.
For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1424 users visited in the last hour