| Previous CloneSet | Next CloneSet | Back to Main Report |
| Clone Mass | Clones in CloneSet | Parameter Count | Clone Similarity | Syntax Category [Sequence Length] |
|---|---|---|---|---|
| 62 | 2 | 2 | 0.996 | file_input_element_list[2] |
| Clone Abstraction | Parameter Bindings |
| Clone Instance (Click to see clone) | Line Count | Source Line | Source File |
|---|---|---|---|
| 1 | 62 | 16 | Bio/AlignAce/Parser.py |
| 2 | 62 | 16 | Bio/Motif/Parsers/AlignAce.py |
| ||||
class AlignAceConsumer:
"""
The general purpose consumer for the AlignAceScanner.
Should be passed as the consumer to the feed method of the AlignAceScanner. After 'consuming' the file, it has the list of motifs in the motifs property.
"""
def __init__(self):
self.motifs = [ ]
self.current_motif = None
self.param_dict = None
def parameters(self,line):
self.param_dict = { }
def parameter(self,line):
par_name = line.split("=")[0].strip( )
par_value = line.split("=")[1].strip( )
self.param_dict[par_name] = par_value
def sequences(self,line):
self.seq_dict = [ ]
def sequence(self,line):
seq_name = line.split("\t")[1]
self.seq_dict.append(seq_name)
def motif(self,line):
self.current_motif = Motif( )
self.motifs.append(self.current_motif)
self.current_motif.alphabet = IUPAC.unambiguous_dna
def motif_hit(self,line):
seq = Seq(line.split("\t")[0],IUPAC.unambiguous_dna)
self.current_motif.add_instance(seq)
def motif_score(self,line):
self.current_motif.score = float(line.split( )[ -1])
def motif_mask(self,line):
self.current_motif.set_mask(line.strip("""
\\c""" ))
def noevent(self,line):
pass
def version(self,line):
self.ver = line
def command_line(self,line):
self.cmd_line = line
class AlignAceParser(AbstractParser):
"""Parses AlignAce data into a sequence of Motifs.
"""
def __init__(self):
"__init__(self)"
self._scanner = AlignAceScanner( )
self._consumer = AlignAceConsumer( )
def parse(self,handle):
"parse(self, handle)"
self._scanner.feed(handle,self._consumer)
return self._consumer.motifs
|
| ||||
class AlignAceConsumer:
"""
The general purpose consumer for the AlignAceScanner.
Should be passed as the consumer to the feed method of the AlignAceScanner. After 'consuming' the file, it has the list of motifs in the motifs property.
"""
def __init__(self):
self.motifs = [ ]
self.current_motif = None
self.param_dict = None
def parameters(self,line):
self.param_dict = { }
def parameter(self,line):
par_name = line.split("=")[0].strip( )
par_value = line.split("=")[1].strip( )
self.param_dict[par_name] = par_value
def sequences(self,line):
self.seq_dict = [ ]
def sequence(self,line):
seq_name = line.split("\t")[1]
self.seq_dict.append(seq_name)
def motif(self,line):
self.current_motif = Motif( )
self.motifs.append(self.current_motif)
self.current_motif.alphabet = IUPAC.unambiguous_dna
def motif_hit(self,line):
seq = Seq(line.split("\t")[0],IUPAC.unambiguous_dna)
self.current_motif.add_instance(seq)
def motif_score(self,line):
self.current_motif.score = float(line.split( )[ -1])
def motif_mask(self,line):
self.current_motif.set_mask(line.strip("""
\\c""" ))
def noevent(self,line):
pass
def version(self,line):
self.ver = line
def command_line(self,line):
self.cmd_line = line
class AlignAceParser(AbstractParser):
"""Parses AlignAce data into a sequence of Motifs.
"""
def __init__(self):
"__init__(self)"
self._scanner = AlignAceScanner( )
self._consumer = AlignAceConsumer( )
def parse(self,handle):
"parse(self, handle)"
self._scanner.feed(handle,self._consumer)
return self._consumer
|
| |||
class AlignAceConsumer:
"""
The general purpose consumer for the AlignAceScanner.
Should be passed as the consumer to the feed method of the AlignAceScanner. After 'consuming' the file, it has the list of motifs in the motifs property.
"""
def __init__(self):
self.motifs = [ ]
self.current_motif = None
self.param_dict = None
def parameters(self,line):
self.param_dict = { }
def parameter(self,line):
par_name = line.split("=")[0].strip( )
par_value = line.split("=")[1].strip( )
self.param_dict[par_name] = par_value
def sequences(self,line):
self.seq_dict = [ ]
def sequence(self,line):
seq_name = line.split("\t")[1]
self.seq_dict.append(seq_name)
def motif(self,line):
self.current_motif = Motif( )
self.motifs.append(self.current_motif)
self.current_motif.alphabet = IUPAC.unambiguous_dna
def motif_hit(self,line):
seq = Seq(line.split("\t")[0],IUPAC.unambiguous_dna)
self.current_motif.add_instance(seq)
def motif_score(self,line):
self.current_motif.score = float(line.split( )[ -1])
def motif_mask(self,line):
self.current_motif.set_mask(line.strip("""
\\c""" ))
def noevent(self,line):
pass
def version(self,line):
self.ver = line
def command_line(self,line):
self.cmd_line = line
class AlignAceParser(AbstractParser):
"""Parses AlignAce data into a sequence of Motifs.
"""
def __init__(self):
"__init__(self)"
self._scanner = AlignAceScanner( )
self._consumer = AlignAceConsumer( )
def parse(self,handle):
"parse(self, handle)"
self._scanner.feed(handle,self._consumer)
return [[#variable60189c40]]. [[#variable60189b00]]
|
| CloneAbstraction |
| Parameter Index | Clone Instance | Parameter Name | Value |
|---|---|---|---|
| 1 | 1 | [[#60189c40]] | self |
| 1 | 2 | [[#60189c40]] | self._consumer |
| 2 | 1 | [[#60189b00]] | _consumer |
| 2 | 2 | [[#60189b00]] | motifs |