tsibley

use strict;
use warnings;
use Benchmark qw< cmpthese >;

my @elements = 1..50;

cmpthese(100000, {
    hash => sub {
         map { $_->{bar} }
        sort { $a->{foo} <=> $b->{foo} }

tsibley

use strict;
use warnings;
package ReportRequire;

sub import {
  my (undef, @targets) = @_;
  @targets = map { s{::}{/}g; "$_.pm" } @targets;

  unshift @INC, sub {
    my ($self, $filename) = @_;

tsibley

BINS 		:= sponge pee
PERLSCRIPTS := chronic
MANS 		:= $(BINS:=.1) $(PERLSCRIPTS:=.1)
PREFIX 		:= /usr/local

selected := PREFIX=$(PREFIX) BINS="$(BINS)" PERLSCRIPTS="$(PERLSCRIPTS)" MANS="$(MANS)"

all:
	make all $(selected)

tsibley

#!/usr/bin/env perl
use strict;
use warnings;

use Getopt::Long;
use File::Basename qw(basename);
use List::MoreUtils qw(any);

my $PROC = $^O eq 'linux' ? 'gnome-session' : 'ssh-agent';
my $USER = getlogin();

tsibley

Keybase proof

I hereby claim:

• I am tsibley on github.
• I am trs (https://keybase.io/trs) on keybase.
• I have a public key whose fingerprint is F725 2810 4751 90A7 4083 D8D5 B1E6 B89F B44E 4AA1

To claim this, I am signing this object:

tsibley

cat("\n\n=== df initially\n");
print(df)

cat("\n\n=== df as data frame\n");
df = data.frame(x = c(1,2), y = c(3,4))
print(df)

aFunction = function(df) {
    cat("\n\n=== df in function\n");
    print(df)

tsibley

#!/usr/bin/env perl
use strict;
use warnings;
use 5.018;

use List::Util qw< sum min max >;
use Bio::Cigar;

my ($file, $region) = @ARGV;
my @region = split /-/, $region =~ s/^.+://r;

tsibley

A Puzzling Error

Today I noticed the following in the error logs of a small webservice I run at work:

Last alignment is non-null!  It should be the empty alignment of the bogus sequence.
  at lib/Bio/WebService/LANL/SequenceLocator.pm line 456.
Alignment is <
 Query ERRRNTATCR RESPNDENCE BETWEENNAM ESANDSEQS  39
 .:::: . : . . : .: .

tsibley

#!/bin/bash
# From the releases mentioned in cpanfile.snapshot, filter out those mentioned in `carton tree`
if ! grep --version | grep -q GNU; then
    echo "GNU grep is required; BSD grep is too feeble"
    exit 1
fi

grep -vFf <(carton tree | grep -oP '(?<=\().+(?=\))') <(grep -P '^  \S' cpanfile.snapshot) | cut -c 3-

tsibley

#!/usr/bin/env perl
# Given a string and a number of tolerable mismatches, generate a list of
# regexes for all possible combinations.  Optionally anchor each regex either
# to the beginning (^) or end ($).  For example:
#
#   $ generate-mismatch-regexes ATCG 2 '^'
#   ^ATCG
#   ^.TCG
#   ^A.CG
#   ^AT.G