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Nikolas Pontikos pontikos

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pontikos / genecards_scraper.py
Created July 26, 2016 10:38
genecards python scraper uses selenium and phantomjs to circumvent Incapsula
from __future__ import print_function
import sys
import re
from selenium import webdriver
from random import randint
from time import sleep
dr = webdriver.PhantomJS()
#dr.get('http://www.genecards.org')
@pontikos
pontikos / bs_download.py
Created February 1, 2017 16:42
Basespace downloader, obtains urls which you can then wget
import sys
import requests
# print urls of fastq files to download
# obtain access token by following instructions here:
# https://support.basespace.illumina.com/knowledgebase/articles/403618-python-run-downloader
AccessToken=sys.argv[1]
# user
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pontikos / three-column.R
Created May 14, 2017 19:38
Convert distance matrix to 3 column matrix
melt(data.matrix(X))->m2
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pontikos / CADD.sh
Last active January 15, 2019 16:28
nicer cadd script than the one provided
#!/bin/bash
#CADDpath="`dirname \"$0\"`"
#CADDpath="`( cd \"$CADDpath/..\" && pwd )`"
set +x
CADDpath=/share/apps/genomics/CADD_v1.3/
if [ -z "$VEPpath" ] ; then source ${CADDpath}/bin/config.sh; fi
echo $VEPpath
NCORES=`expr $(lscpu | grep '^CPU(s):' | cut -f2 -d: | tr -d ' ') - 2`