def _get_b2g_blast(self, input_fpath, goblast_settings):
'It gets a chopped blast ready for use with blast2go'
if 'kind' in goblast_settings:
db_kind = goblast_settings['kind']
else:
db_kind = guess_blastdb_kind(goblast_settings['path'])
seq_type = scrape_info_from_fname(input_fpath)['st']
blast_program = guess_blast_program(seq_type, db_kind,
prefer_tblastx=True)
blastdb = goblast_settings['path']
project_dir = self._project_settings['General_settings']['project_path']
blast = backbone_blast_runner(query_fpath=input_fpath,
project_dir=project_dir,
blast_program=blast_program,
blast_db=blastdb,
dbtype=db_kind,
threads=self.threads)
chop_big_xml, num_items = True, 2
if chop_big_xml:
#chopped_blast = open('/tmp/blast_itemized.xml', 'w')
chopped_blast = NamedTemporaryFile(suffix='.xml')
for blast_parts in xml_itemize(blast, 'Iteration', num_items):
chopped_blast.write(blast_parts)
chopped_blast.flush()
return chopped_blast
else:
return open(blast)
def test_xml_itemize_by_chunks():
'''It tests xml itemize but with more than one item'''
string = '<h><t><c>1</c><c>2</c><c>3</c><c>4</c><c>5</c></t></h>'
xml = StringIO.StringIO(string)
xmls = list(xml_itemize(xml, 'c', num_items=2))
assert xmls[0] == '<h><t><c>1</c><c>2</c></t></h>'
assert xmls[1] == '<h><t><c>3</c><c>4</c></t></h>'
assert xmls[2] == '<h><t><c>5</c></t></h>'
assert len(xmls) == 3
def test_xml_itemize():
'''It tests xml itemize'''
string = '<h><t><c></c><c></c></t></h>'
xml = StringIO.StringIO(string)
cont = 0
for result in xml_itemize(xml, 'c'):
assert result == '<h><t><c></c></t></h>'
cont += 1
assert cont == 2
def xml_iprscan_parser_iter(fhand):
"""It parses an iprscan xml result file.
It's an iterator that yields the different protein sections
"""
parser = make_parser()
handler = InterProHandler()
parser.setContentHandler(handler)
for protein_section in xml_itemize(fhand, "protein"):
fhand = StringIO.StringIO(protein_section)
parser.parse(fhand)
yield handler.get_protein()