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davfre /
Last active Aug 29, 2015
Convert JGI gtf-like annotation file to GTF2.2 format
#!/usr/bin/perl -w
use strict;
use warnings;
This script converts a JGI gtf-like file:
scaffold_1 JGI exon 46078 46218 . + . name "gw.1.597.1"; transcriptId 65742
davfre /
Last active Aug 29, 2015
Filter a textfile to output only the lines where a given identifier is present.
use strict;
my $usage = "cat input.gtf | $! idlist.txt > filtered.gtf\n";
my %ids;
my $FN_idlist = $ARGV[0];
open my $FH_idlist, "<", $FN_idlist or die $usage;
# read id list to memory
davfre /
Last active Nov 21, 2019
SAM and BAM filtering oneliners
davfre /
Last active Dec 7, 2019
git commandline cheat-sheet
davfre / IBM Tivoli 6.4.0 Installation on Ubuntu
Last active Jul 9, 2019
Installation procedure for the IBM Tivoli 6.4.0 client for Ubuntu 12.10.
View IBM Tivoli 6.4.0 Installation on Ubuntu

The procedure below documents how to install the IBM Tivoli client on the Ubuntu linux distribution. The steps involve unpacking the distributed RPMs, removing and renaming a few files in the resulting folders, and editing and adding a few configuration text files, followed by packaging .deb files for installation.

Adapted from

Current versions: IBM Tivoli 6.4.0 Ubuntu 12.10

View .tmux.conf
#go to last active window (hit C-b twice)
bind-key C-b last-window
#split windows key bindings
unbind %
bind | split-window -h
bind - split-window -v
#status bar
set -g status-bg black
set -g status-fg white
set -g status-left '#[fg=green]#H'
davfre / Pattern.t
Created Nov 14, 2012
Test script for AppliedProgramming course, Exercise 6
View Pattern.t
use Test::More tests => 15;
use Pattern;
use Restriction;
use strict;
use warnings;
# sequences for testing
my $testsequence0 = "AAAAAAAAAACGATCTAAAAAAA" ; #should not match
my $testsequence1 = "AAAAAAAAAAAGATCCAAAAAAA" ; #should match
my $testsequence2 = "AAAAAAAAAAGGATCTAAAAAAA" ; #should match
davfre /
Created Oct 31, 2012
# Multiple pipes to/from one process
View .screenrc
escape ^Tt
caption string "%?%F%{= Bk}%? %C%A %D %d-%m-%Y %{= kB} %t%= %?%F%{= Bk}%:%{= wk}%? %n "
shell bash
defscrollback 10000
hardstatus on
hardstatus alwayslastline
hardstatus string '%{= kG}[ %{G}%H %{g}][%= %{= kw}%?%-Lw%?%{r}(%{W}%n*%f%t%?(%u)%?%{r})%{w}%?%+Lw%?%?%= %{g}][%{B} %d/%m %{W}%c %{g}]'
vbell off
davfre /
Created Oct 17, 2012
Applied Programming course examples
# Template for Applied Programming course exercise Day2 Exercise 1
use strict;
use warnings;
my @sampleA = (65,69,70,63,70,68);
my @sampleB = (102,95,98,110);
my @sampleC = (112,115,113,109,95,98,100);
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