perl-for-reysenbach-lab
dotfiles
| perl-for-reysenbach-lab | dotfiles | |
|---|---|---|
| 3 | 5 | |
| 3 | 1 | |
| - | - | |
| 10.0 | 7.9 | |
| over 1 year ago | about 2 months ago | |
| Perl | Shell | |
| - | MIT License |
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perl-for-reysenbach-lab
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Faster tetranucleotide (k-mer) frequencies!
I saw Jennifer's post about re-writing her perl scripts in python and how she saw a 2.5 times improvement.
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Calculating tetranucleotide (k-mer) frequencies
In 2016 I wrote a Perl script for the Reysenbach lab that calculates k-mer frequencies, for all k-mers in a given sequence. It was made public soon after, and you can find get_kmer_frequencies.pl on my Github page.
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Get GC Content
I wrote a Perl script that calculates GC content for all the sequences in a fasta file back in 2010 for the Reysenbach Lab, and it was made publicly available soon after. You can find get_gc_content.pl on GitHub (https://github.com/jmeneghin/perl-for-reysenbach-lab)
dotfiles
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Why Automate?
Folks enjoy citing XKCD 1205 in automation discussions because it does a great job illustrating the opportunity time cost of automation. The time spent to code a new solution for an already solved problem doesn't help solve business goals until after the investment pays off.
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I setup my terminal for max productivity
as framed in the introduction of this article, https://xkcd.com/1205 is hard to ignore whenever i'm spending time configuring a tool in the name of "productivity"
but i just got nushell properly set up and i've realised that the table doesn't capture the whole dynamic: there's more to work than time trade-offs when new tools enable entirely new types of tasks.
nushell makes working with structured data fun and so i've started benchmarking my code and quickly doing performance analysis - something i was rarely doing before.
you can still ultimately reduce this down to time saved, i suppose, but as a person who's generally skeptical of terminal tweaking as procrastination in disguise, i can highly recommend giving nushell a go.
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Blog Posts, Sorted by Sleep
I believe most of us sleep fewer than 3 times per day, so writing down times and doing a few subtractions and a little data entry once a week should be under 1 min/day to have everything digitised. (that said, https://xkcd.com/1205/ suggests it'd be worth spending up to 21 hours to fully automate)
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Faster tetranucleotide (k-mer) frequencies!
There are no more obvious or easy gains here. Any more work is likely to yield small returns. Go outside, have a life or at the least consult the relevant chart.
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Apple built iCloud to store billions of databases
It isn't as polished as whatever first-party solution Apple has the potential to develop, but I just use OneDrive to restore my personal data + chezmoi to reprovision my dotfiles and it works pretty well.
About every six months I do a fire drill and completely factory reset my macbook. Takes about 20 minutes (with only 5 minutes of actual keyboard attention required) for me to go from a fresh device to one that has all my apps and developer tools ready to roll.
https://github.com/eh8/dotfiles
What are some alternatives?
faster-perl-for-reysenbach - Tracks the progress of making old Perl scripts faster and more maintainable. Working from Meneghin's perl-for-reysenbach-lab repository of bioinformatics scripts.