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from Martel import Dispatch
from Bio import Search, StdHandler
class BuildSearch(Dispatch.Dispatcher):
def __init__(self):
Dispatch.Dispatcher.__init__(self,
prefix = "bioformat:",
remap = {
"bioformat:hit": "bioformat:hit_description_block",
}
)
self.acquire(StdHandler.Handle_hsp(self.add_hsp))
self.acquire(StdHandler.Handle_search_header(self.add_header))
self.acquire(StdHandler.Handle_search_table(self.add_table))
self.acquire(StdHandler.Handle_search_info(self.add_stats))
def start_(self, name, attrs):
self.algorithm = None
self.query = None
self.database = None
self.table = []
self.hits = []
self.parameters = {}
self.statistics = {}
def end_(self, name):
self.document = None
self.document = Search.Search(
self.algorithm,
self.query,
self.database,
self.table,
self.hits,
self.parameters,
self.statistics)
def start_hit(self, name, attrs):
self.hit_description = None
self.hit_length = None
self.hsps = []
def end_hit(self, name):
self.hits.append(Search.Hit("XXX SPAM", self.hit_description,
"XXX EGGS", self.hit_length,
self.algorithm, self.hsps))
def add_hsp(self, hsp_values, hsp_handler, strands, frames):
self.hsps.append(Search.HSP(hsp_handler.query_seq,
hsp_handler.homology_seq,
hsp_handler.subject_seq,
# XXX strand and frame!
(hsp_handler.query_start_loc,
hsp_handler.query_end_loc),
(hsp_handler.subject_start_loc,
hsp_handler.subject_end_loc),
hsp_handler.query_name,
hsp_handler.subject_name,
self.algorithm,
hsp_values))
def add_table(self, table):
self.table = [Search.TableInfo(*x) for x in table]
def add_header(self, info):
self.algorithm = Search.Algorithm(info["appname"],
info["appversion"])
self.database = Search.Database(info["dbname"],
info["db_num_letters"],
info["db_num_sequences"])
self.query = Search.Query("XXX spam", "XXX eggs",
info["query_description"],
info["query_size"])
def add_stats(self, parameters, statistics):
self.parameters = parameters
self.statistics = statistics
StdHandler.add_text_block_handler(BuildSearch, "hit_description",
"join-description", "join|fixspaces",
"hit_description")
StdHandler.add_int_handler(BuildSearch, "hit_length", "hit_length")
make_builder = BuildSearch
|
