| import numpy as np | |
| import itertools | |
| def rle(x): | |
| where = np.flatnonzero | |
| x = np.asarray(x) | |
| n = len(x) | |
| if n == 0: | |
| return np.array([], dtype=int) | |
| starts = np.r_[0, where(~np.isclose(x[1:], x[:-1], equal_nan=True)) + 1] |
| # https://www.topbug.net/blog/2013/04/14/install-and-use-gnu-command-line-tools-in-mac-os-x/ | |
| brew install coreutils | |
| brew install binutils | |
| brew install diffutils | |
| brew install ed --with-default-names | |
| brew install findutils --with-default-names | |
| brew install gawk | |
| brew install gnu-indent --with-default-names | |
| brew install gnu-sed --with-default-names |
Resolving missing link to libcrypto openssl on OSX from: http://stackoverflow.com/questions/38670295/brew-refusing-to-link-openssl
brew update
brew install openssl
ln -s /usr/local/opt/openssl/lib/libcrypto.1.0.0.dylib /usr/local/lib/
ln -s /usr/local/opt/openssl/lib/libssl.1.0.0.dylib /usr/local/lib/
| end_dist=30000 | |
| chrom_I=15072434 | |
| chrom_II=15279421 | |
| chrom_III=13783801 | |
| chrom_IV=17493829 | |
| chrom_V=20924180 | |
| chrom_X=17718942 | |
| # Special thanks for insights from flowingdata.com regarding this. | |
| library(plotKML) | |
| library(plyr) | |
| library(dplyr) | |
| library(fpc) | |
| num_locations <- 5 | |
| # Usage: Place this script in the directory containing your runkeeper data. You can run from terminal using 'Rscript map_runkeeper.R', or |
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)
| ## See http://gettinggeneticsdone.blogspot.com/2013/06/customize-rprofile.html | |
| ## Load packages | |
| library(BiocInstaller) | |
| ## Don't show those silly significanct stars | |
| options(show.signif.stars=FALSE) | |
| ## Do you want to automatically convert strings to factor variables in a data.frame? | |
| ## WARNING!!! This makes your code less portable/reproducible. |
| import requests | |
| def doi2bib(doi): | |
| """ | |
| Return a bibTeX string of metadata for a given DOI. | |
| """ | |
| url = "http://dx.doi.org/" + doi | |
| headers = {"accept": "application/x-bibtex"} |
| #!/usr/local/bin/perl | |
| # | |
| # | |
| # Perl script find_closest_worm_paralogs4.pl | |
| # Written by Avril Coghlan ([email protected]) | |
| # 16-Feb-09. | |
| # | |
| # This perl script finds the bootstrap value for the | |
| # clade containing a pair of C. elegans paralogs in a family (where | |
| # there is no other gene in that clade, ie. they are each other's |
