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package RangeTree; | |
use strict; | |
use warnings; | |
use Set::IntervalTree; | |
sub new { | |
my $class = shift; | |
my $self = {}; # container is a hash with seqnames as keys |
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" | |
"http://www.w3.org/TR/html4/strict.dtd"> | |
<html> | |
<head> | |
<title>miRDeep2</title> | |
<!-- CSS code --> | |
<style type="text/css"> | |
body{ | |
font: .75em Arial,sans-serif; | |
background: #FFFFFF; |
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" | |
"http://www.w3.org/TR/html4/strict.dtd"> | |
<html> | |
<head> | |
<title>miRDeep2</title> | |
<!-- CSS code --> | |
<style type="text/css"> | |
body{ | |
font: .75em Arial,sans-serif; | |
background: #FFFFFF; |
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Hello World! |
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Run in single end mode: | |
========== _____ _ _ ____ _____ ______ _____ | |
===== / ____| | | | _ \| __ \| ____| /\ | __ \ | |
===== | (___ | | | | |_) | |__) | |__ / \ | | | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | | |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ | |
v1.5.2 | |
//========================== featureCounts setting ===========================\\ |
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#!/bin/sh | |
set -eu | |
# WARNING: you need to adapt the dependency list first | |
# | |
# shell script allowing to install all CRISPRCasFinder.pl-v4.2's dependencies | |
# | |
# same version than CRISPRCasFinder.pl, here 4.2.17 | |
# authors: David Couvin, Fabrice Leclerc, Claire Toffano-Nioche | |
# adapted to non sudo install by M. Dondrup |
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CURDIR=`pwd` | |
LOGFILE=$CURDIR/macsysfinder-install.log # give the logfile a proper name | |
# if [ -e $LOGFILE ]; then rm $LOGFILE ; fi # no need to delete the file each time | |
mkdir -p bin | |
mkdir -p src | |
#install vmatch | |
echo " downloading and compiling of Vmatch" >> $LOGFILE | |
echo "change directory to $CURDIR/src" >> $LOGFILE | |
cd src |
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#!/usr/bin/env perl | |
use strict; | |
use warnings; | |
use Bio::Tools::GFF; | |
use Bio::SeqFeatureI; | |
my %fstore1 = (); | |
my %fstore2 = (); | |
my %conflicts = (); |
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library(Rpdb) | |
library(pdist) | |
#mypdb <- read.pdb("SCARB_S361384_results_itasser/1dve-rmsd.pdb", HETATM = T, ATOM = T, MODEL = 1:2) | |
my.pdist <- function(x,y) { | |
ret <- as.matrix(pdist(x,y), nrow = nrow(x), ncol=nrow(y)) | |
dimnames(ret) <- list(row.names(x), row.names(y)) | |
return(list(ret)) |
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MODEL 1 | |
ATOM 1 C1 UNK 1 46.878 21.312-121.026 1.00 0.00 C | |
ATOM 2 C2 UNK 1 46.008 21.716-122.189 1.00 0.00 C | |
ATOM 3 C3 UNK 1 46.381 22.574-123.243 1.00 0.00 C | |
ATOM 4 C4 UNK 1 47.629 23.170-123.351 1.00 0.00 C | |
ATOM 5 C5 UNK 1 47.990 24.006-124.415 1.00 0.00 C | |
ATOM 6 N1 UNK 1 47.231 24.376-125.447 1.00 0.00 N | |
ATOM 7 C6 UNK 1 47.918 25.174-126.264 1.00 0.00 C | |
ATOM 8 C7 UNK 1 47.497 25.776-127.450 1.00 0.00 C | |
ATOM 9 C8 UNK 1 46.216 25.625-127.970 1.00 0.00 C |
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