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View check_all_studies_imported.py
"""
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("https://api.github.com/repos/cBioPortal/datahub/contents/public")
View test_iframe.html
<html>
<body>
I'm on github
</body>
</html>
View mrna_distribution_cbioportal.ipynb
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View hotspots_categories.ipynb
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View WorldPopulations.html
<!doctype HTML>
<meta charset = 'utf-8'>
<html>
<head>
<link rel='stylesheet' href='data:text/css;base64,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
View show_missing_rows_between_2_tables.py
"""
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
inodb / gene_lengths.md
Last active Dec 22, 2016
Gene lengths in Jupyter notebook
View gene_lengths.md

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 "http://grch37.rest.ensembl.org/xrefs/symbol/homo_sapiens/"{gene} -H 'Content-type:application/json' | \
            jq '.[0].id' | tr -d '"' | \
@inodb
inodb / 20161012_frontend_dev_workshop.md
Last active Oct 12, 2016
Frontend dev workshop 20161012
View 20161012_frontend_dev_workshop.md

20161002 Frontend dev workshop

Set up cbioportal-frontend

Check out the README at https://github.com/cBioPortal/cbioportal-frontend/ 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
inodb / deletion_fastq_simulation_ensembl_api.md
Last active Jun 3, 2016
Generate deletions of arbitrary length in hg19 using ensembl rest api
View deletion_fastq_simulation_ensembl_api.md

Generate reads with deletions of arbitrary length using ensembl rest api

for del_size in 10 30 50 70 90 150 300 600
do
  chr=17
  start_pos=4126000
  read_length=100
  ens_url="http://grch37.rest.ensembl.org/sequence/region/human/"
  qual=$(python -c "print 'A'*${read_length}")
  (
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