[BioPython] More results at NCBI Search
João Rodrigues
anaryin at gmail.com
Fri Sep 21 20:33:55 UTC 2007
Sure I can :) Must warn though, that I have 2 weeks of "python-ing" so the
code *could* be clearer! Oh, and some of it is in Portuguese because it's
for personal use..
# NCBI Retriever
import os
import sys
# What should I look for?
query = raw_input('Qual a expressao que deseja procurar?\n..: ')
# Where should I look for?
print 'Em qual das bases de dados deseja procurar?'
databases = {1: 'PubMed', 2: 'Nucleotide', 3:
'Protein',4:'Genome',5:'Structure'}
choice = raw_input('[1] PubMed\n[2] Nucleotide\n[3] Protein\n[4] Genome\n[5]
Structure\n..: ')
if int(choice) not in databases.keys():
print 'Escolha Inválida'
sys.exit()
search_database = databases[int(choice)]
# Quit playing around, let s search!
from Bio.WWW import NCBI
search_command = 'Search'
results = NCBI.query(search_command , search_database, term = query,
doptcmdl = 'FASTA')
# Where should I save the results?
import time
actual_date = str(time.localtime()[0])+str(time.localtime()[1])+str(
time.localtime()[2])
results_file_name = os.path.join(os.getcwd(),
str(query)+'_'+str(actual_date)+".txt")
results_file = open(results_file_name, 'w')
results_file.write(results.read())
results_file.close()
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