leipzig

#Directories
SOURCEDIR := sources
FASTQDIR := fastq
DECODEDDIR := decoded
BAMDIR := bam
SCRIPTDIR := scripts
TRIMMEDDIR := trimmed

#Parameters
MIN_LENGTH := 15

leipzig

library("plyr")
library("XML")
library("ggplot2")

#Concatenate SQL-style
concat<-function(...,sep="",collapse=NULL){
  strings<-list(...)
  #NULL, NA
  if(
    all(unlist(llply(strings,length))>0)

leipzig

function mycd()
{
    #if this directory is writable then write to directory-based history file
    #otherwise write history in the usual home-based history file                    
    tmpDir=$PWD
    echo "#"`date '+%s'` >> $HISTFILE
    echo $USER' has exited '$PWD' for '$@ >> $HISTFILE
    builtin cd "$@" # do actual cd
    if [ -w $PWD ]; then export HISTFILE="$PWD/.dir_bash_history"; touch $HISTFILE; chmod --silent 777 $HISTFILE;
    else export HISTFILE="$HOME/.bash_history";

leipzig

#!/usr/bin/perl
use strict;
use Carp;
use Carp::Assert;
use Getopt::Std;
use File::Slurp;

my %opt;
my $opt_string = 'o:d:rh';

leipzig

#!/usr/bin/perl
use strict;
use Getopt::Std;
use LWP::UserAgent;
use HTTP::Request::Common;

my %opt;
my $opt_string = 'hcms';

getopts( "$opt_string", \%opt ) or &usage();

leipzig

#!/usr/bin/expect -f
#Upload a file to an Aspera server, filling in the passphrase field
#Usage: ./autopass.sh mybigassfile
set arg1 [lindex $argv 0]
set timeout -1
spawn ascp -i sra-rsakey-putty.ppk -k 1 -Qr -l300M $arg1 user@asperadomain.ncbi.nlm.nih.gov:protected/
expect "Passphrase for key \"rsa-key-blahblah\":"
send "mypassword\r"
expect "Completed"
#add the file you successfully uploaded to a log

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#bin  chrom	chromStart	chromEnd	ix	n	size	type	bridge
0	chr1	124535434	142535434	1271	N	18000000	heterochromatin	no
23	chr1	121535434	124535434	1270	N	3000000	centromere	no
76	chr1	3845268	3995268	47	N	150000	contig	no
85	chr1	13219912	13319912	154	N	100000	contig	no
89	chr1	17125658	17175658	196	N	50000	clone	yes
101	chr1	29878082	30028082	337	N	150000	contig	no
188	chr1	120697156	120747156	1263	N	50000	clone	yes
188	chr1	120936695	121086695	1265	N	150000	contig	no
188	chr1	121485434	121535434	1269	N	50000	clone	no

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default: vcffilesdone

clean:
        rm disease_loci/*/*vcf
        rm vcffilesdone

#gene cards list of known disease loci
diseaseloci.html:
        curl http://www.genecards.org/cgi-bin/listdiseasecards.pl?type=full > diseaseloci.html
#scrape loci

leipzig

#!/usr/bin/perl                                                                                                                                                                                                                                                                                                                                             
use LWP::UserAgent;
use HTTP::Request::Common;

my $userAgent = LWP::UserAgent->new(timeout => 1800); #a half-hour                                                                                                                                                                                                                                                                                          

my $request = POST 'http://mitomaster.mitomap.org/cgi-bin/websrvc.cgi', [
    gb => $ARGV[0],
    fileType => 'id',
    output => 'hsd'

leipzig

---

title: "Template for writing scientific papers in R markdown" author: "Petr Keil, pkeil@seznam.cz" date: "11/1/2015" output: pdf_document: fig_caption: yes keep_tex: yes number_sections: yes html_document: