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Ino de Bruijn inodb

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Check if studies on datahub are imported in live public portal
Currently comparing study folder name on datahub vs live public portal studies
endpoint. Should prolly look at actual `cancer_study_identifier: study_name` in
meta_study.txt file, but this seems to work.
import requests
public_study_folders = requests.get("")
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View WorldPopulations.html
<!doctype HTML>
<meta charset = 'utf-8'>
<link rel='stylesheet' href='data:text/css;base64,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
Output rows from table1 that are missing from table2 i.e. table1 - table2, use
given columns to determine 'missing'
import argparse
import pandas as pd
import sys
def output_missing_rows(t1, t2, join_columns, delimiter, output_only_columns):
inodb /
Last active Dec 22, 2016
Gene lengths in Jupyter notebook

Gene lenghts from ENSEMBL REST API

Use inside notebook (uses ! syntax):

import json
import pandas as pd

def get_gene_length(gene):
    gene_info = \
        !curl -s ""{gene} -H 'Content-type:application/json' | \
            jq '.[0].id' | tr -d '"' | \
inodb /
Last active Oct 12, 2016
Frontend dev workshop 20161012

20161002 Frontend dev workshop

Set up cbioportal-frontend

Check out the README at for up to date info

Try to make a component

Make a new component that show the Patient Information on a single line, instead of in a table. We would like that line to be in the PatientHeader component. You could name it PatientInline similar to SampleInline.

inodb /
Last active Jun 3, 2016
Generate deletions of arbitrary length in hg19 using ensembl rest api

Generate reads with deletions of arbitrary length using ensembl rest api

for del_size in 10 30 50 70 90 150 300 600
  qual=$(python -c "print 'A'*${read_length}")
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