def module_2_api_call():
organism = 'aedes aegypti'
geneIDs = [
'AAEL003439', 'AAEL011411', 'AAEL012522', 'AAEL012774', 'AAEL012864',
'AAEL013263'
]
ied = ",".join(geneIDs)
#print(ied[:-1])
Entrez.email = sys.argv[1]
handle = Entrez.esearch(db="pubmed", retmax=13, id=ied, term=organism)
record = Entrez.read(handle)
handle.close()
print(record['IdList'])
final['PubMedIDs'] = record['IdList']
id_list = record['IdList']
papers = fetch_details(id_list)
print(papers)
'''for i, paper in enumerate(papers):
print()'''
final['ids'] = []
final['seq'] = []
final['papers_id'] = record['IdList']
client = ensembl_rest.EnsemblClient()
for genes in geneIDs:
temp = client.sequence_id(genes)
final['ids'].append(genes)
final['seq'].append(temp['seq'])
# --- File Verification and Import
isFile("fetch_genes.py")
path2intronDB = sys.argv[2]
isFile(path2intronDB)
import fetch_genes
# --- START ---
species = (sys.argv[1] if (len(sys.argv) > 1) else 'gallus gallus')
print("\nSpecies:", species)
client = ensembl_rest.EnsemblClient()
# --- Fetch information of the s in Gallus gallus
print('\nFetching chromosome data...', end=" ")
chrom_data, genome_info = fetch_genes.chromosomes_info(species=species)
print("DONE.")
# --- Fetch the ids of all the genes in the Gallus Gallus genome
print('\nFetching all gene IDs...')
all_genes = sum(
(fetch_genes.genes_in_chrom(species, chrom, chrom_data[chrom]['length'])
for chrom in chrom_data), [])