def search(self, organism='', options='', batch_size=50, progress=True):
Entrez.email = self.email
search_handle = Entrez.esearch(db="nucleotide",
term=organism+options,
usehistory="y")
search_results = Entrez.read(search_handle)
search_handle.close()
webenv = search_results["WebEnv"]
query_key = search_results["QueryKey"]
gi_list = search_results["IdList"]
retmax = int(search_results["RetMax"])
count = int(search_results["Count"])
if count == 0:
return
assert retmax == len(gi_list)
### Download data referred to in the previous search in batches
tinyseqxml = organism + '.tseqxml'
if not os.path.isfile(tinyseqxml):
widgets = [tinyseqxml + "\t", Percentage(), ' ',
Bar(marker=RotatingMarker()),
' ', ETA(), ' ', FileTransferSpeed(unit='r')]
out_handle = open(tinyseqxml, "w")
pbar = ProgressBar(widgets=widgets,
maxval=count,
term_width=int(self.columns) - 20)
for start in range(0, count, batch_size):
#end = min(count, start + batch_size)
#print("Going to download record %i to %i" % (start+1, end))
fetch_handle = Entrez.efetch(db="nucleotide",
rettype="fasta",
retmode="xml",
retstart=start,
retmax=batch_size,
webenv=webenv,
query_key=query_key)
data = fetch_handle.read()
fetch_handle.close()
out_handle.write(data)
status = (start + 1) / float(count)
if progress and pbar.seconds_elapsed == 0:
pbar.start()
if status > 0.001 and progress:
pbar.term_width = int(self.columns) - 20
pbar.update(status * count)
if progress:
pbar.finish()
out_handle.close()
## At this point, file may be a stream of multiple XML documents.
### Do not parse as one single XML document.
### Beautiful Soup PUNCH! (Think Donkey Kong)
start = CURRENT_MILLI_TIME()
soup = BeautifulSoup(open(tinyseqxml, "r"), "lxml")
end = CURRENT_MILLI_TIME()
print "Finished Parsing XML in " + str(end - start) + " ms"
return soup.find_all('tseq')
