def search(self,start,end):
search_command = 'Search'
search_database = 'Protein'
return_format = 'GenPept'
Protein_gi_line = re.compile(r'Protein\<\/a\>')
CDS_gi_line = re.compile(r'CDS\<\/a\>')
pattern_gi = re.compile(r'val=(\d*)')
j=1
if start<1:
start =1
if end >len(self.accs) or end == 0:
end = len(self.accs)
for k in range(start-1,end):
sys.stderr.write("No " + repr(j) + ": " + self.accs[k] +'\n')
j=j+1
try :
result_handle = NCBI.query(search_command, search_database, term=self.accs[k], doptcmdl = return_format)
tmp=result_handle.readline()
sys.stdout.write(tmp)
while tmp:
sys.stdout.write(tmp)
if Protein_gi_line.search(tmp):
protein_gi=pattern_gi.search(tmp).group(1)
sys.stderr.write( "fetching "+protein_gi + '\n')
protein_handle=NCBI.query('Text',search_database, uid=protein_gi,dopt=return_format)
proteinfile.write(protein_handle.read())
if CDS_gi_line.search(tmp):
CDS_gi=pattern_gi.search(tmp).group(1)
#sys.stderr.write( "fetching " + CDS_gi + '\n')
#CDS_handle=NCBI.query('Text','nucleotide', uid=CDS_gi,dopt='GenBank')
#CDSfile.write(CDS_handle.read())
tmp = result_handle.readline()
except:
print "Entrez query error"
See http://www.ncbi.nlm.nih.gov/entrez/query/static/linking.html for
more help understanding the parameters passed.
This also requires a web browser to run -- either netscape or lynx
are supported in this example."""
# standard library
import os
# biopython
from Bio.WWW import NCBI
search_command = 'Search'
search_database = 'Nucleotide'
return_format = 'FASTA'
search_term = 'Cypripedioideae'
my_browser = 'lynx'
result_handle = NCBI.query(search_command, search_database, term = search_term,
doptcmdl = return_format)
result_file_name = os.path.join(os.getcwd(), 'results.html')
result_file = open(result_file_name, 'w')
result_file.write(result_handle.read())
result_file.close()
if my_browser == 'lynx':
os.system('lynx -force_html ' + result_file_name)
elif my_browser == 'netscape':
os.system('netscape file:' + result_file_name)
more help understanding the parameters passed.
This also requires a web browser to run -- either netscape or lynx
are supported in this example."""
# standard library
import os
# biopython
from Bio.WWW import NCBI
search_command = 'Search'
search_database = 'Nucleotide'
return_format = 'FASTA'
search_term = 'Cypripedioideae'
my_browser = 'lynx'
result_handle = NCBI.query(search_command,
search_database,
term=search_term,
doptcmdl=return_format)
result_file_name = os.path.join(os.getcwd(), 'results.html')
result_file = open(result_file_name, 'w')
result_file.write(result_handle.read())
result_file.close()
if my_browser == 'lynx':
os.system('lynx -force_html ' + result_file_name)
elif my_browser == 'netscape':
os.system('netscape file:' + result_file_name)
