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inodb/gene_lengths.md

Last active December 22, 2016 17:09
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Gene lengths in Jupyter notebook
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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 '"' | \
            xargs -I GENEID curl -s "http://grch37.rest.ensembl.org/lookup/id/"GENEID -H 'Content-type:application/json'
    d = json.loads(gene_info[0])
    return max(d['start'], d['end']) - min(d['start'], d['end'])

gene_lengths = pd.Series({gene: get_gene_length(gene) for gene in df.reset_index().GENE.unique()})
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