Moderator: Alex Reynolds

gravatar for Alex Reynolds
Alex Reynolds21k
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20,810
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Location:
Seattle, WA USA
Website:
http://dropbit.com/
Twitter:
AlexReynolds
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Google Scholar Page
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an hour ago
Joined:
7 years, 10 months ago
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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

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Comment: C: Extract gene lists using two files
... 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 Reynolds21k
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Comment: C: Extract gene lists using two files
... 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 Reynolds21k
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Comment: C: Extract gene lists using two files
... 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 Reynolds21k
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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 Reynolds21k
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Comment: C: Extract gene lists using two files
... 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 Reynolds21k
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Answer: C: search text in one file and then replace with text from another file
... 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 Reynolds21k
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Comment: C: search text in one file and then replace with text from another file
... 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 Reynolds21k
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Answer: A: Extract gene lists using two files
... 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 Reynolds21k • updated 1 day ago by genomax34k
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Comment: C: search text in one file and then replace with text from another file
... 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 Reynolds21k
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Comment: C: how to find snps within 1Kb from the gene
... 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 Reynolds21k

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
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: How To Sort Bed Format File
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
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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?

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