Reshape mutation matrix for use by core-service repository about cancer-data HOT 3 CLOSED

I agree this is an important step, but I think we will want to do it slightly differently than in #35. I think we should do the processing in 2.TCGA-process.ipynb where the mutation data starts out in a melted format. I also think we may want to add some additional columns like mutation severity which will be useful for the frontend in the future.

Until we sort these things out, can you use the workaround here for cognoma/core-service#42 (which is a super high priority PR, so let's complete that ASAP):

path = 'mutation-matrix.tsv.bz2'
read_file = bz2.open(path , 'rt')
reader = csv.DictReader(read_file, delimiter='\t')
for row in reader:
    sample_id = row.pop('sample_id')
    for entrez_gene_id, mutation_status in row.items():
        if mutation_status == '1':
            # Create mutation from entrez_gene_id, sample_id
reader.close()

from cancer-data.

bz2 module for the win! So simple this way!!

from cancer-data.

See #35.

from cancer-data.