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python-biopython  1.60
Public Member Functions | Private Attributes
Bio.Blast.NCBIStandalone._ParametersConsumer Class Reference
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Public Member Functions

def start_parameters
def matrix
def gap_penalties
def num_hits
def num_sequences
def num_extends
def num_good_extends
def num_seqs_better_e
def hsps_no_gap
def hsps_prelim_gapped
def hsps_prelim_gapped_attempted
def hsps_gapped
def query_length
def database_length
def effective_hsp_length
def effective_query_length
def effective_database_length
def effective_search_space
def effective_search_space_used
def frameshift
def threshold
def window_size
def dropoff_1st_pass
def gap_x_dropoff
def gap_x_dropoff_final
def gap_trigger
def blast_cutoff
def end_parameters

Private Attributes

 _params

Detailed Description

Definition at line 1305 of file NCBIStandalone.py.


Member Function Documentation

Definition at line 1468 of file NCBIStandalone.py.

01468 
01469     def blast_cutoff(self, line):
01470         score, bits = _re_search(
01471             r"S2: (\d+) \(\s*([0-9,.]+) bits\)", line,
01472             "I could not find the blast cutoff in line\n%s" % line)
01473         self._params.blast_cutoff = _safe_int(score), _safe_float(bits)
        

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Definition at line 1382 of file NCBIStandalone.py.

01382 
01383     def database_length(self, line):
01384         self._params.database_length, = _get_cols(
01385             line.lower(), (-1,), ncols=4, expected={0:"length", 2:"database:"})
01386         self._params.database_length = _safe_int(self._params.database_length)

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Definition at line 1444 of file NCBIStandalone.py.

01444 
01445     def dropoff_1st_pass(self, line):
01446         score, bits = _re_search(
01447             r"X1: (\d+) \(\s*([0-9,.]+) bits\)", line,
01448             "I could not find the dropoff in line\n%s" % line)
01449         self._params.dropoff_1st_pass = _safe_int(score), _safe_float(bits)
        

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Definition at line 1399 of file NCBIStandalone.py.

01399 
01400     def effective_database_length(self, line):
01401         self._params.effective_database_length, = _get_cols(
01402             line.lower(), (-1,), ncols=5, expected={1:"length", 3:"database:"})
01403         self._params.effective_database_length = _safe_int(
01404             self._params.effective_database_length)
        

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Definition at line 1387 of file NCBIStandalone.py.

01387 
01388     def effective_hsp_length(self, line):
01389         self._params.effective_hsp_length, = _get_cols(
01390             line, (-1,), ncols=4, expected={1:"HSP", 2:"length:"})
01391         self._params.effective_hsp_length = _safe_int(
01392             self._params.effective_hsp_length)

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Definition at line 1393 of file NCBIStandalone.py.

01393 
01394     def effective_query_length(self, line):
01395         self._params.effective_query_length, = _get_cols(
01396             line, (-1,), ncols=5, expected={1:"length", 3:"query:"})
01397         self._params.effective_query_length = _safe_int(
01398             self._params.effective_query_length)

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Definition at line 1405 of file NCBIStandalone.py.

01405 
01406     def effective_search_space(self, line):
01407         self._params.effective_search_space, = _get_cols(
01408             line, (-1,), ncols=4, expected={1:"search"})
01409         self._params.effective_search_space = _safe_int(
01410             self._params.effective_search_space)

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Definition at line 1411 of file NCBIStandalone.py.

01411 
01412     def effective_search_space_used(self, line):
01413         self._params.effective_search_space_used, = _get_cols(
01414             line, (-1,), ncols=5, expected={1:"search", 3:"used:"})
01415         self._params.effective_search_space_used = _safe_int(
01416             self._params.effective_search_space_used)

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Reimplemented in Bio.Blast.NCBIStandalone._PSIBlastConsumer, and Bio.Blast.NCBIStandalone._BlastConsumer.

Definition at line 1474 of file NCBIStandalone.py.

01474 
01475     def end_parameters(self):
01476         pass
01477     

Definition at line 1417 of file NCBIStandalone.py.

01417 
01418     def frameshift(self, line):
01419         self._params.frameshift = _get_cols(
01420            line, (4, 5), ncols=6, expected={0:"frameshift", 2:"decay"})

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Definition at line 1312 of file NCBIStandalone.py.

01312 
01313     def gap_penalties(self, line):
01314         x = _get_cols(
01315             line, (3, 5), ncols=6, expected={2:"Existence:", 4:"Extension:"})
01316         self._params.gap_penalties = map(_safe_float, x)

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Definition at line 1462 of file NCBIStandalone.py.

01462 
01463     def gap_trigger(self, line):
01464         score, bits = _re_search(
01465             r"S1: (\d+) \(\s*([0-9,.]+) bits\)", line,
01466             "I could not find the gap trigger in line\n%s" % line)
01467         self._params.gap_trigger = _safe_int(score), _safe_float(bits)
        

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Definition at line 1450 of file NCBIStandalone.py.

01450 
01451     def gap_x_dropoff(self, line):
01452         score, bits = _re_search(
01453             r"X2: (\d+) \(\s*([0-9,.]+) bits\)", line,
01454             "I could not find the gap dropoff in line\n%s" % line)
01455         self._params.gap_x_dropoff = _safe_int(score), _safe_float(bits)
        

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Definition at line 1456 of file NCBIStandalone.py.

01456 
01457     def gap_x_dropoff_final(self, line):
01458         score, bits = _re_search(
01459             r"X3: (\d+) \(\s*([0-9,.]+) bits\)", line,
01460             "I could not find the gap dropoff final in line\n%s" % line)
01461         self._params.gap_x_dropoff_final = _safe_int(score), _safe_float(bits)

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Definition at line 1372 of file NCBIStandalone.py.

01372 
01373     def hsps_gapped(self, line):
01374         self._params.hsps_gapped, = _get_cols(
01375             line, (-1,), ncols=6, expected={3:"gapped"})
01376         self._params.hsps_gapped = _safe_int(self._params.hsps_gapped)
        

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Definition at line 1355 of file NCBIStandalone.py.

01355 
01356     def hsps_no_gap(self, line):
01357         self._params.hsps_no_gap, = _get_cols(
01358             line, (-1,), ncols=9, expected={3:"better", 7:"gapping:"})
01359         self._params.hsps_no_gap = _safe_int(self._params.hsps_no_gap)

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Definition at line 1360 of file NCBIStandalone.py.

01360 
01361     def hsps_prelim_gapped(self, line):
01362         self._params.hsps_prelim_gapped, = _get_cols(
01363             line, (-1,), ncols=9, expected={4:"gapped", 6:"prelim"})
01364         self._params.hsps_prelim_gapped = _safe_int(
01365             self._params.hsps_prelim_gapped)

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Definition at line 1366 of file NCBIStandalone.py.

01366 
01367     def hsps_prelim_gapped_attempted(self, line):
01368         self._params.hsps_prelim_gapped_attempted, = _get_cols(
01369             line, (-1,), ncols=10, expected={4:"attempted", 7:"prelim"})
01370         self._params.hsps_prelim_gapped_attempted = _safe_int(
01371             self._params.hsps_prelim_gapped_attempted)

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Definition at line 1309 of file NCBIStandalone.py.

01309 
01310     def matrix(self, line):
01311         self._params.matrix = line[8:].rstrip()

Definition at line 1333 of file NCBIStandalone.py.

01333 
01334     def num_extends(self, line):
01335         if line.find('1st pass') != -1:
01336             x, = _get_cols(line, (-4,), ncols=9, expected={2:"extensions:"})
01337             self._params.num_extends = _safe_int(x)
01338         else:
01339             x, = _get_cols(line, (-1,), ncols=4, expected={2:"extensions:"})
01340             self._params.num_extends = _safe_int(x)

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Definition at line 1341 of file NCBIStandalone.py.

01341 
01342     def num_good_extends(self, line):
01343         if line.find('1st pass') != -1:
01344             x, = _get_cols(line, (-4,), ncols=10, expected={3:"extensions:"})
01345             self._params.num_good_extends = _safe_int(x)
01346         else:
01347             x, = _get_cols(line, (-1,), ncols=5, expected={3:"extensions:"})
01348             self._params.num_good_extends = _safe_int(x)
        

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Definition at line 1317 of file NCBIStandalone.py.

01317 
01318     def num_hits(self, line):
01319         if line.find('1st pass') != -1:
01320             x, = _get_cols(line, (-4,), ncols=11, expected={2:"Hits"})
01321             self._params.num_hits = _safe_int(x)
01322         else:
01323             x, = _get_cols(line, (-1,), ncols=6, expected={2:"Hits"})
01324             self._params.num_hits = _safe_int(x)

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Definition at line 1349 of file NCBIStandalone.py.

01349 
01350     def num_seqs_better_e(self, line):
01351         self._params.num_seqs_better_e, = _get_cols(
01352             line, (-1,), ncols=7, expected={2:"sequences"})
01353         self._params.num_seqs_better_e = _safe_int(
01354             self._params.num_seqs_better_e)

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Definition at line 1325 of file NCBIStandalone.py.

01325 
01326     def num_sequences(self, line):
01327         if line.find('1st pass') != -1:
01328             x, = _get_cols(line, (-4,), ncols=9, expected={2:"Sequences:"})
01329             self._params.num_sequences = _safe_int(x)
01330         else:
01331             x, = _get_cols(line, (-1,), ncols=4, expected={2:"Sequences:"})
01332             self._params.num_sequences = _safe_int(x)

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Definition at line 1377 of file NCBIStandalone.py.

01377 
01378     def query_length(self, line):
01379         self._params.query_length, = _get_cols(
01380             line.lower(), (-1,), ncols=4, expected={0:"length", 2:"query:"})
01381         self._params.query_length = _safe_int(self._params.query_length)
        

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Definition at line 1306 of file NCBIStandalone.py.

Definition at line 1421 of file NCBIStandalone.py.

01421 
01422     def threshold(self, line):
01423         if line[:2] == "T:":
01424             #Assume its an old stlye line like "T: 123"
01425             self._params.threshold, = _get_cols(
01426                 line, (1,), ncols=2, expected={0:"T:"})
01427         elif line[:28] == "Neighboring words threshold:":
01428             self._params.threshold, = _get_cols(
01429                 line, (3,), ncols=4, expected={0:"Neighboring", 1:"words", 2:"threshold:"})
01430         else:
01431             raise ValueError("Unrecognised threshold line:\n%s" % line)
01432         self._params.threshold = _safe_int(self._params.threshold)
        

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Definition at line 1433 of file NCBIStandalone.py.

01433 
01434     def window_size(self, line):
01435         if line[:2] == "A:":
01436             self._params.window_size, = _get_cols(
01437                 line, (1,), ncols=2, expected={0:"A:"})
01438         elif line[:25] == "Window for multiple hits:":
01439             self._params.window_size, = _get_cols(
01440                 line, (4,), ncols=5, expected={0:"Window", 2:"multiple", 3:"hits:"})
01441         else:
01442             raise ValueError("Unrecognised window size line:\n%s" % line)
01443         self._params.window_size = _safe_int(self._params.window_size)
        

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Member Data Documentation

Definition at line 1307 of file NCBIStandalone.py.


The documentation for this class was generated from the following file: