| <p> | |
| My programming language of preference is python for the simple reason that I feel I write better code faster with it then I do with other languages. However also has a lot of nice tricks and idioms to do things well. And partly as a reminder to myself to use them, and partly because I thought this might be of general interest I have put together this collection of some of my favourite idioms. I am also putting this on <a href="https://gist.github.com/codefisher/9d7993ddbf404c505128">gist.github.com</a> so that anyone that wants to contribute there own things can, and I will try and keep this post up to date. | |
| </p> | |
| <h2>enumerate</h2> | |
| <p> | |
| A fairly common thing to do is loop over a list while also keeping track of what index we are up to. Now we could use a <code>count</code> variable, but python gives us a nicer syntax for this with the <code>enumerate()</code> function. | |
| <script src="https://gist.github.com/codefisher/9d7993ddbf404c505128.js?file=enumerate.py"></script> |
| # Hello, and welcome to makefile basics. | |
| # | |
| # You will learn why `make` is so great, and why, despite its "weird" syntax, | |
| # it is actually a highly expressive, efficient, and powerful way to build | |
| # programs. | |
| # | |
| # Once you're done here, go to | |
| # http://www.gnu.org/software/make/manual/make.html | |
| # to learn SOOOO much more. |
| /* | |
| For any 1<k<=64, let mask=(1<<k)-1. hash_64() is a bijection on [0,1<<k), which means | |
| hash_64(x, mask)==hash_64(y, mask) if and only if x==y. hash_64i() is the inversion of | |
| hash_64(): hash_64i(hash_64(x, mask), mask) == hash_64(hash_64i(x, mask), mask) == x. | |
| */ | |
| // Thomas Wang's integer hash functions. See <https://gist.github.com/lh3/59882d6b96166dfc3d8d> for a snapshot. | |
| uint64_t hash_64(uint64_t key, uint64_t mask) | |
| { | |
| key = (~key + (key << 21)) & mask; // key = (key << 21) - key - 1; |
SAM and BAM filtering one-liners
@author: David Fredman, [email protected] (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/
Please extend with additional/faster/better solutions via a pull request!
BWA mapping (using piping for minimal disk I/O)
Original link: http://www.concentric.net/~Ttwang/tech/inthash.htm
Taken from: http://web.archive.org/web/20071223173210/http://www.concentric.net/~Ttwang/tech/inthash.htm
Reformatted using pandoc
Thomas Wang, Jan 1997
last update Mar 2007
| /* | |
| * I add this to html files generated with pandoc. | |
| */ | |
| html { | |
| font-size: 100%; | |
| overflow-y: scroll; | |
| -webkit-text-size-adjust: 100%; | |
| -ms-text-size-adjust: 100%; | |
| } |
Attention: the list was moved to
https://github.com/dypsilon/frontend-dev-bookmarks
This page is not maintained anymore, please update your bookmarks.
| This is the list of exit codes for wget: | |
| 0 No problems occurred | |
| 1 Generic error code | |
| 2 Parse error — for instance, when parsing command-line options, the .wgetrc or .netrc… | |
| 3 File I/O error | |
| 4 Network failure | |
| 5 SSL verification failure | |
| 6 Username/password authentication failure | |
| 7 Protocol errors |
| #!/bin/bash | |
| # Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress] | |
| # | |
| # Deinterleaves a FASTQ file of paired reads into two FASTQ | |
| # files specified on the command line. Optionally GZip compresses the output | |
| # FASTQ files using pigz if the 3rd command line argument is the word "compress" | |
| # | |
| # Can deinterleave 100 million paired reads (200 million total | |
| # reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s) | |
| # |
