Jim Hester jimhester
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| #!/usr/bin/env perl | |
| use warnings;use strict; | |
| my ($header,$sequence); | |
| $header = <>; | |
| chomp $header; | |
| while(my $line = <>){ | |
| chomp $line; | |
| if($line =~ /^>/){ |
jimhester
/ parseREBASE.pl
Created
July 31, 2012 15:29
Restriction enzyme regular expression performance
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| my %sites; | |
| while(<>){ | |
| next if( 1 .. /Rich Roberts/); | |
| next unless /\S/; | |
| my(@names) = split /[\s\)\(]+/; | |
| my $site = IUB_to_regexp(uc($names[-1])); | |
| if(not exists $sites{$site} and not exists $sites{$site}){ |
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| ```{r error,dev='svg'} | |
| library(ggplot2) | |
| ggplot(movies,aes(x=rating)) + geom_histogram(aes(fill=..count..)) | |
| ``` |
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| #include <fstream> | |
| #include <Rcpp.h> | |
| using namespace Rcpp; | |
| // [[Rcpp::export]] | |
| CharacterVector read_fasta(std::string file) { | |
| CharacterVector records; | |
| std::ifstream in(file.c_str()); | |
| in.get(); // remove first '>' |
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| require(Rcpp) | |
| require(GenomicRanges) | |
| sourceCpp('read_gff.cpp') | |
| read_gff = function(file, grouping='feature_id', attribute_sep='=') { | |
| data = data.frame(lapply(gff2df(file, attribute_sep), all_numeric, what="vector")) | |
| if(!grouping %in% colnames(data)){ | |
| stop(paste(grouping, "does not exist in", file, ", valid columns are", paste(colnames(data), collapse=" "))) | |
| } | |
| stopifnot(grouping %in% colnames(data)) | |
| lapply(split(data, factor(data$seqid)), function(df) { |
jimhester
/ knitr_report.css
Created
March 8, 2013 21:09
knitr Rmd reports - custom css and javascript header
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| #toc { | |
| top: 0px; | |
| left: 0px; | |
| height: 100%; | |
| position: fixed; | |
| width: 150px; | |
| padding-top: 20px; | |
| color: white; | |
| } |
jimhester
/ java.hprof.2.1.24.txt
Last active
December 19, 2015 23:59
IGV over X11 hprof results for version 2.1.24 and 2.3.12
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| JAVA PROFILE 1.0.1, created Fri Jul 19 08:47:09 2013 | |
| Copyright (c) 2003, 2005, Oracle and/or its affiliates. All rights reserved. | |
| Redistribution and use in source and binary forms, with or without | |
| modification, are permitted provided that the following conditions | |
| are met: | |
| - Redistributions of source code must retain the above copyright | |
| notice, this list of conditions and the following disclaimer. |
jimhester
/ team_colors.r
Created
August 19, 2013 18:13
Get Hex team colors for NBA, NFL, NHL, and MLB from http://teamcolors.arc90.com/ for use in R.
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| url = 'http://teamcolors.arc90.com/' | |
| library(httr) | |
| get_colors = function(league=c('NBA', 'NFL', 'NHL', 'MLB')){ | |
| league = match.arg(league) | |
| color_data = parse_html(GET('http://teamcolors.arc90.com/')) | |
| rbind.fill(xpathApply(color_data, | |
| paste('//*[@id="', league, '"]/li[@class="team"]', sep=''), | |
| parse_team)) |
jimhester
/ .gitignore
Last active
December 21, 2015 19:39
— forked from hadley/.gitignore
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| .Rproj.user | |
| .Rhistory | |
| .RData | |
| *.Rproj | |
| *.html |
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| withOptions <- function(optlist, expr) | |
| { | |
| oldopt <- options(optlist) | |
| on.exit(options(oldopt)) | |
| expr <- substitute(expr) | |
| eval.parent(expr) | |
| } | |
| less = function(x) { | |
| withOptions(list(pager='less', dplyr.print_min=.Machine$integer.max, width=10000L), page(x, method='print')) |
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