def parse(query_sequence, blast_output_file, self_hit, hitid_format):
'''
Processes a blast xml formated output into a {BlastResult} object.
@param: query_sequence
@pdef: sequence of the query protein/nucleotide.
@ptype: {String}
@param: blast_output_file
@pdef: output file from BLAST.
@ptype: {String}
@param: self_hit
@pdef: when _True_ if the query is found in the database, it is
retrieved.
@pdefault: _False_
@ptype: {Boolean}
@param: hitid_format
@pdef: format of the name of the hit. If given a wrong option,
it defaults to 'single'
@pdefault: 'single'
@poptions: 'single' -> first word of the name,
'double' -> first two words of the hit name,
'all' -> all the text in the hit name
@ptype: {String}
@raises: {BlastError} if there are problems while parsing the XML file.
@returns: {BlastResult}
'''
f = File(blast_output_file)
s = BeautifulSoup(f.read())
h = BlastHeader(version = str(s.find('blastoutput_version').string),
matrix = str(s.find('parameters_matrix').string),
gap_open = int(s.find('parameters_gap-open').string),
gap_extend = int(s.find('parameters_gap-extend').string),
database = str(s.find('blastoutput_db').string),
self_hit = self_hit)
b = BlastResult(query_name = str(s.find('blastoutput_query-def').string),
query_sequence = query_sequence,
header = h)
SBIg.alert('debug', BlastParser(), b.str_blast_header())
error_bool = False
error_str = []
for iteration in s.find_all('iteration'):
iternum = int(iteration.find('iteration_iter-num').string)
for hit in iteration.find_all('hit'):
hit_name = BlastParser.hit_name(str(hit.find('hit_def').string), hitid_format)
hit_lenth = int(hit.find("hit_len").string)
for subhit in hit.find_all("hsp"):
data = BlastParser.parse_subhit(subhit)
r = BlastHit(hit = [hit_name, hit_lenth],
sequences = [data['qs'], data['hs'], data['sc']],
sequence_inits = [data['qp'], data['hp']],
iteration = iternum,
stats = [data['hi'], data['h+'],
data['hg'], data['ev']])
if not BlastParser.same_query_hit_names(b.query, hit_name, self_hit):
dbug_info = 'Added hit {0} in iteration {1}'
SBIg.alert('debug', BlastParser(), dbug_info.format(hit_name, r.iteration))
b.add_hit(r)
if not r.are_segments_ok:
error_bool = True
error_str.append("Check the alignment's fragmentation")
error_str.append("for the query %s with %s\n".format(b.query, hit_name))
error_str.append("{0}\n".format(r))
b.set_last_iteration()
if error_bool:
SBIg.warn(BlastParser(), error_str)
be = BlastError()
raise be.parse_error()
return b
