Mercurial > repos > earlhaminst > gstf_preparation

comparison gstf_preparation.py @ 3:7e11a7f4bdba draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 77ed525b753e34d3e9dd4f07a239592ce764f7e6-dirty
author earlhaminst
date Fri, 24 Nov 2017 12:32:39 -0500
parents a36645976342
children 284f64ad9d43
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2:19644996bc2a 3:7e11a7f4bdba
218 218
219 def write_gene_dict_to_db(conn, gene_dict): 219 def write_gene_dict_to_db(conn, gene_dict):
220 cur = conn.cursor() 220 cur = conn.cursor()
221 221
222 for gene in gene_dict.values(): 222 for gene in gene_dict.values():
223 if gene is None:
224 # This can happen when loading a JSON file from Ensembl
225 continue
223 gene_id = gene['id'] 226 gene_id = gene['id']
224 cur.execute('INSERT INTO gene (gene_id, gene_symbol, species, gene_json) VALUES (?, ?, ?, ?)', 227 cur.execute('INSERT INTO gene (gene_id, gene_symbol, species, gene_json) VALUES (?, ?, ?, ?)',
225 (gene_id, gene.get('display_name', None), gene['species'], json.dumps(gene))) 228 (gene_id, gene.get('display_name', None), gene['species'], json.dumps(gene)))
226 229
227 if "Transcript" in gene: 230 if "Transcript" in gene: