def populate(self, box, schema_name):
for child in box.get_children():
box.remove(child)
functions.Functions(self.main, self.conn, box, schema_name,
self.schema_store)
sequences.Sequences(self.main, self.conn, box, schema_name)
tables.Tables(self.main, self.conn, box, schema_name,
self.schema_store)
views.Views(self.main, self.conn, box, schema_name, self.schema_store)
def load(in_name, models):
fname = None
seq = None
constraint = ""
both_strands = False
cands = []
count = -1
tries = [0,0]
if( not in_name is None ):
fi = open( in_name )
else:
fi = sys.stdin
for line in fi:
line = line.strip()
if( line.startswith( "##seq = " ) ):
seq = line.split( "=" )[1].strip()
elif( line.startswith( "##seq_file = " ) ):
fname = line.split( "=" )[1].strip()
elif( line.startswith( "##constraint = " ) ):
constraint = line.split( "=" )[1].strip()
elif( line.startswith( "##both_strands = " ) ):
both_strands = (line.split( "=" )[1].strip() == 'YES')
elif( line.startswith( "##sequences = " ) ):
count = int(line.split( "=" )[1].strip())
elif( line.startswith( "##tests_all = " ) ):
tries[0] = int(line.split( "=" )[1].strip())
elif( line.startswith( "##tests_pairs = " ) ):
tries[1] = int(line.split( "=" )[1].strip())
elif( line.startswith( "#" ) or (line == "") ):
continue
else:
cands.append( candidates.CandidateParser.parse( line, models ) )
seqs = sequences.Sequences(fname=fname, seq=seq, both_strands=both_strands)
if( not in_name is None ):
fi.close()
return( seqs, cands, constraint, count, tries )
help="Minimum bpp to accept a candidate.")
#parser.add_option( "--min-evalue", action="store", dest="min_evalue", default=None, type="float", help="Minimum -log(e-value) to accept candidate." )
parser.add_option("--constraint",
action="store",
dest="constraint",
default=None,
type="string",
help="File containing secondary structure constraints.")
(options, args) = parser.parse_args()
#
# Read the input sequences from wherever they came
#
seqs = sequences.Sequences(fname=((len(args) > 0) and args[0] or None),
both_strands=options.both_strands)
#
# Configure and initialize the search class
#
# set the default values for 'win_len' and 'win_step'
config.win_len = options.win_len
if (options.win_step is None):
config.win_step = int(config.win_len / 2)
else:
config.win_step = options.win_step
# Read the secondary structure constraints if they exist
if (not options.constraint is None):
with open(filename, 'r') as f:
lines = f.readlines()
x = 0
while x < len(lines):
name = lines[x].strip('\n').lstrip('>')
x += 1
emissions = lines[x].strip('\n').lstrip(' ')
x += 1
hiddens = lines[x].strip('\n').lstrip('# ')
x += 2
data[name] = dict(X=emissions, Z=hiddens)
return data;
def __str__(self):
return str(self.sequences)
def __len__(self):
return len(self.sequences)
def get(self):
return self.sequences
def get_by_key(self, key):
return self.sequences[key]
if __name__ == "__main__":
import sequences
SEQUENCEFILE = '../sequences-project2.txt'
sequences = sequences.Sequences(SEQUENCEFILE)
print sequences