User: Lee Katz

gravatar for Lee Katz
Lee Katz2.9k
Reputation:
2,880
Status:
Trusted
Location:
Atlanta, GA
Website:
http://leekatz.com/
Twitter:
lskatz
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Google Scholar Page
Last seen:
2 months ago
Joined:
8 years, 1 month ago
Email:
l*****@gmail.com

I am a bioinformatics scientist at Centers for Disease Control and Prevention (CDC).  I am interested in evolution of bacterial pathogens including Vibrio and Listeria.  What I write here does not necessarily reflect the opinions or views of CDC.

Posts by Lee Katz

<prev • 366 results • page 1 of 37 • next >
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Comment: C: Script To Calculate A Distance Matrix Based On Tree File
... This was amazingly fast, and my jaw dropped ...
written 5 months ago by Lee Katz2.9k
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Answer: A: Bioperl gff3 : How to print non gff3 feature as "###" using Bio::Tools::GFF
... Here is the code that actually works after I did some digging. It's a little bit of a hack but I don't believe it will cause any problems. Also I changed it to `Bio::FeatureIO` which I think is a little more mainstream. In this one-liner, `###` is printed to the output file after each input featu ...
written 2.1 years ago by Lee Katz2.9k
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Answer: A: Bioperl gff3 : How to print non gff3 feature as "###" using Bio::Tools::GFF
... Jean-Karim is correct that the GFF module will probably only output features. However, you probably can manually write to the file in your perl script! There is a method called `$obj->fh` which returns the filehandle of your GFF object. Therefore you could write to the file as desired. For ex ...
written 2.1 years ago by Lee Katz2.9k
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Answer: A: Pfge Prediction Based On Wgs
... I was looking for this answer yet again but didn't see anything yet again, curiously. Here is the script I've developed over time for anyone else who might be looking. https://github.com/lskatz/lskScripts/blob/master/pfgeOnGenome.pl Run with --help for usage. ...
written 2.1 years ago by Lee Katz2.9k
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Comment: C: Portable genome browser
... I appreciate the idea @Jean, but @genomax2 is right that I would like to send something interactive over email. I can package and prepare something, but it needs to be ready to go when the recipient opens it from email. ...
written 2.1 years ago by Lee Katz2.9k
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Comment: C: Bioperl gff3 : How to print non gff3 feature as "###" using Bio::Tools::GFF
... Could you write an example of what you'd like to see in the GFF3 file? ...
written 2.1 years ago by Lee Katz2.9k
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Comment: C: Portable genome browser
... Unfortunately, running this and probably any other JS-based browser locally will trigger cross-site errors, as I have learned from Genoverse this morning. I thought that a JS-based client would be the optimal solution; however, there is a fundamental security obstacle. ...
written 2.1 years ago by Lee Katz2.9k
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Comment: C: Portable genome browser
... This is beautiful. I will try it out. ...
written 2.1 years ago by Lee Katz2.9k
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Comment: C: Portable genome browser
... No, I am not allowed to host a website at my work unfortunately, and I am ethically disinclined to redistribute IGV. The files have to go through email. ...
written 2.1 years ago by Lee Katz2.9k
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Comment: C: Portable genome browser
... I love IGV and use it; however it is not immediately clear how I could save a session complete with features and a reference assembly such that my colleagues could open the session from their email. I am also not clear how I'd zip all of IGV and send it over email when my size limit is 20MB and the ...
written 2.1 years ago by Lee Katz2.9k

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