CloneSet11


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Clone
Mass
Clones in
CloneSet
Parameter
Count
Clone
Similarity
Syntax Category
[Sequence Length]
53640.962or_test
Clone AbstractionParameter Bindings
Clone Instance
(Click to see clone)
Line CountSource Line
Source File
15160
Bio/Align/Applications/_Dialign.py
2557
Bio/Align/Applications/_Muscle.py
3564
Bio/Align/Applications/_Muscle.py
4584
Bio/Align/Applications/_Muscle.py
5592
Bio/Align/Applications/_Muscle.py
65120
Bio/Align/Applications/_Muscle.py
75128
Bio/Align/Applications/_Muscle.py
85136
Bio/Align/Applications/_Muscle.py
95172
Bio/Align/Applications/_Muscle.py
105179
Bio/Align/Applications/_Muscle.py
115187
Bio/Align/Applications/_Muscle.py
125195
Bio/Align/Applications/_Muscle.py
135253
Bio/Align/Applications/_Muscle.py
145260
Bio/Align/Applications/_Muscle.py
155272
Bio/Align/Applications/_Muscle.py
16668
Bio/Align/Applications/_TCoffee.py
17674
Bio/Align/Applications/_TCoffee.py
18434
Bio/Sequencing/Applications/_Novoalign.py
19438
Bio/Sequencing/Applications/_Novoalign.py
20442
Bio/Sequencing/Applications/_Novoalign.py
21546
Bio/Sequencing/Applications/_Novoalign.py
22453
Bio/Sequencing/Applications/_Novoalign.py
23457
Bio/Sequencing/Applications/_Novoalign.py
24563
Bio/Sequencing/Applications/_Novoalign.py
25468
Bio/Sequencing/Applications/_Novoalign.py
26572
Bio/Sequencing/Applications/_Novoalign.py
27577
Bio/Sequencing/Applications/_Novoalign.py
28488
Bio/Sequencing/Applications/_Novoalign.py
29592
Bio/Sequencing/Applications/_Novoalign.py
305104
Bio/Sequencing/Applications/_Novoalign.py
314109
Bio/Sequencing/Applications/_Novoalign.py
324119
Bio/Sequencing/Applications/_Novoalign.py
334125
Bio/Sequencing/Applications/_Novoalign.py
344131
Bio/Sequencing/Applications/_Novoalign.py
354137
Bio/Sequencing/Applications/_Novoalign.py
364141
Bio/Sequencing/Applications/_Novoalign.py
Clone Instance
1
Line Count
5
Source Line
160
Source File
Bio/Align/Applications/_Dialign.py

            _Option(["-thr","thr"],["input"],
                    lambda x:isinstance(x,types.IntType),0,"Threshold T = x.",0)


Clone Instance
2
Line Count
5
Source Line
57
Source File
Bio/Align/Applications/_Muscle.py

            #anchorspacing   Integer              32                 Minimum spacing between
            _Option(["-anchorspacing","anchorspacing"],["input"],
                    lambda x:isinstance(x,types.IntType),0,"Minimum spacing between anchor columns",0)


Clone Instance
3
Line Count
5
Source Line
64
Source File
Bio/Align/Applications/_Muscle.py

            #center          Floating point       [1]                Center parameter.
            #                                                        Should be negative.
            _Option(["-center","center"],["input"],
                    lambda x:isinstance(x,types.FloatType),0,"Center parameter - should be negative",0)


Clone Instance
4
Line Count
5
Source Line
84
Source File
Bio/Align/Applications/_Muscle.py

            #diaglength      Integer              24                 Minimum length of
            #                                                        diagonal.
            _Option(["-diaglength","diaglength"],["input"],
                    lambda x:isinstance(x,types.IntType),0,"Minimum length of diagonal",0)


Clone Instance
5
Line Count
5
Source Line
92
Source File
Bio/Align/Applications/_Muscle.py

            #diagmargin      Integer              5                  Discard this many
            #                                                        positions at ends of
            #                                                        diagonal.
            _Option(["-diagmargin","diagmargin"],["input"],
                    lambda x:isinstance(x,types.IntType),0,"Discard this many positions at ends of diagonal",0)


Clone Instance
6
Line Count
5
Source Line
120
Source File
Bio/Align/Applications/_Muscle.py

            #gapopen         Floating point       [1]                The gap open score.
            #                                                        Must be negative.
            _Option(["-gapopen","gapopen"],["input"],
                    lambda x:isinstance(x,types.FloatType),0,"Gap open score - negative number",0)


Clone Instance
7
Line Count
5
Source Line
128
Source File
Bio/Align/Applications/_Muscle.py

            #hydro           Integer              5                  Window size for
            #                                                        determining whether a
            #                                                        region is hydrophobic.
            _Option(["-hydro","hydro"],["input"],
                    lambda x:isinstance(x,types.IntType),0,"Window size for hydrophobic region",0)


Clone Instance
8
Line Count
5
Source Line
136
Source File
Bio/Align/Applications/_Muscle.py

            #hydrofactor     Floating point       1.2                Multiplier for gap
            #                                                        open/close penalties in
            #                                                        hydrophobic regions.
            _Option(["-hydrofactor","hydrofactor"],["input"],
                    lambda x:isinstance(x,types.FloatType),0,"Multiplier for gap penalties in hydrophobic regions",0)


Clone Instance
9
Line Count
5
Source Line
172
Source File
Bio/Align/Applications/_Muscle.py

            #maxhours        Floating point       None.              Maximum time to run in
            #                                                        hours. The actual time
            #                                                        may exceed the
            #                                                        requested limit by a
            #                                                        few minutes. Decimals
            #                                                        are allowed, so 1.5
            #                                                        means one hour and 30
            #                                                        minutes.
            _Option(["-maxhours","maxhours"],["input"],
                    lambda x:isinstance(x,types.FloatType),0,"Maximum time to run in hours",0)


Clone Instance
10
Line Count
5
Source Line
179
Source File
Bio/Align/Applications/_Muscle.py

            #maxiters        Integer 1, 2 ...     16                 Maximum number of
            #                                                        iterations.
            _Option(["-maxiters","maxiters"],["input"],
                    lambda x:isinstance(x,types.IntType),0,"Maximum number of iterations",0)


Clone Instance
11
Line Count
5
Source Line
187
Source File
Bio/Align/Applications/_Muscle.py

            #maxtrees        Integer              1                  Maximum number of new
            #                                                        trees to build in
            #                                                        iteration 2.
            _Option(["-maxtrees","maxtrees"],["input"],
                    lambda x:isinstance(x,types.IntType),0,"Maximum number of trees to build in iteration 2",0)


Clone Instance
12
Line Count
5
Source Line
195
Source File
Bio/Align/Applications/_Muscle.py

            #minbestcolscore Floating point       [1]                Minimum score a column
            #                                                        must have to be an
            #                                                        anchor.
            _Option(["-minbestcolscore","minbestcolscore"],["input"],
                    lambda x:isinstance(x,types.FloatType),0,"Minimum score a column must have to be an anchor",0)


Clone Instance
13
Line Count
5
Source Line
253
Source File
Bio/Align/Applications/_Muscle.py

            #smoothscoreceil Floating point       [1]                Maximum value of column
            #                                                        score for smoothing
            #                                                        purposes.
            _Option(["-smoothscoreceil","smoothscoreceil"],["input"],
                    lambda x:isinstance(x,types.FloatType),0,"Maximum value of column score for smoothing",0)


Clone Instance
14
Line Count
5
Source Line
260
Source File
Bio/Align/Applications/_Muscle.py

            #smoothwindow    Integer              7                  Window used for anchor
            #                                                        column smoothing.
            _Option(["-smoothwindow","smoothwindow"],["input"],
                    lambda x:isinstance(x,types.IntType),0,"Window used for anchor column smoothing",0)


Clone Instance
15
Line Count
5
Source Line
272
Source File
Bio/Align/Applications/_Muscle.py

            #SUEFF           Floating point value 0.1                Constant used in UPGMB
            #                between 0 and 1.                        clustering. Determines
            #                                                        the relative fraction
            #                                                        of average linkage
            #                                                        (SUEFF) vs. nearest-
            #                                                        neighbor linkage (1
            #                                                        SUEFF).
            _Option(["-sueff","sueff"],["input"],
                    lambda x:isinstance(x,types.FloatType),0,"Constant used in UPGMB clustering",0)


Clone Instance
16
Line Count
6
Source Line
68
Source File
Bio/Align/Applications/_TCoffee.py

           _Option(["-gapopen","gapopen"],["input"],
                    lambda x:isinstance(x,types.IntType),0,"Indicates the penalty applied for opening a gap "
                                                           "(negative integer)",0)


Clone Instance
17
Line Count
6
Source Line
74
Source File
Bio/Align/Applications/_TCoffee.py

           _Option(["-gapext","gapext"],["input"],
                    lambda x:isinstance(x,types.IntType),0,"Indicates the penalty applied for extending a "
                                                           "gap. (negative integer)",0)


Clone Instance
18
Line Count
4
Source Line
34
Source File
Bio/Sequencing/Applications/_Novoalign.py

            # Alignment scoring options
            _Option(["-t","threshold"],["input"],
                    lambda x:isinstance(x,types.IntType),0,"Threshold for alignment score",0)


Clone Instance
19
Line Count
4
Source Line
38
Source File
Bio/Sequencing/Applications/_Novoalign.py

            _Option(["-g","gap_open"],["input"],
                    lambda x:isinstance(x,types.IntType),0,"Gap opening penalty [default: 40]",0)


Clone Instance
20
Line Count
4
Source Line
42
Source File
Bio/Sequencing/Applications/_Novoalign.py

            _Option(["-x","gap_extend"],["input"],
                    lambda x:isinstance(x,types.IntType),0,"Gap extend penalty [default: 15]",0)


Clone Instance
21
Line Count
5
Source Line
46
Source File
Bio/Sequencing/Applications/_Novoalign.py

            _Option(["-u","unconverted"],["input"],
                    lambda x:isinstance(x,types.IntType),0,"""Experimental: unconverted cytosines penalty in bisulfite mode

"""                                                        "Default: no penalty",0)


Clone Instance
22
Line Count
4
Source Line
53
Source File
Bio/Sequencing/Applications/_Novoalign.py

            # Quality control and read filtering
            _Option(["-l","good_bases"],["input"],
                    lambda x:isinstance(x,types.IntType),0,"Minimum number of good quality bases [default: log(N_g, 4) + 5]",0)


Clone Instance
23
Line Count
4
Source Line
57
Source File
Bio/Sequencing/Applications/_Novoalign.py

            _Option(["-h","homopolymer"],["input"],
                    lambda x:isinstance(x,types.IntType),0,"Homopolymer read filter [default: 20; disable: negative value]",0)


Clone Instance
24
Line Count
5
Source Line
63
Source File
Bio/Sequencing/Applications/_Novoalign.py

            # Read preprocessing options
            _Option(["-a","adapter3"],["input"],
                    lambda x:isinstance(x,types.StringType),0,"""Strips a 3' adapter sequence prior to alignment.

"""                                                        "With paired ends two adapters can be specified",0)


Clone Instance
25
Line Count
4
Source Line
68
Source File
Bio/Sequencing/Applications/_Novoalign.py

            _Option(["-n","truncate"],["input"],
                    lambda x:isinstance(x,types.IntType),0,"Truncate to specific length before alignment",0)


Clone Instance
26
Line Count
5
Source Line
72
Source File
Bio/Sequencing/Applications/_Novoalign.py

            _Option(["-s","trimming"],["input"],
                    lambda x:isinstance(x,types.IntType),0,"""If fail to align, trim by s bases until they map or become shorter than l.

"""                                                     "Ddefault: 2",0)


Clone Instance
27
Line Count
5
Source Line
77
Source File
Bio/Sequencing/Applications/_Novoalign.py

            _Option(["-5","adapter5"],["input"],
                    lambda x:isinstance(x,types.StringType),0,"""Strips a 5' adapter sequence.

"""                                                        "Similar to -a (adaptor_3), but on the 5' end.",0)


Clone Instance
28
Line Count
4
Source Line
88
Source File
Bio/Sequencing/Applications/_Novoalign.py

            _Option(["-Q","quality"],["input"],
                    lambda x:isinstance(x,types.IntType),0,"Lower threshold for an alignment to be reported [default: 0]",0)


Clone Instance
29
Line Count
5
Source Line
92
Source File
Bio/Sequencing/Applications/_Novoalign.py

            _Option(["-R","repeats"],["input"],
                    lambda x:isinstance(x,types.IntType),0,"""If score difference is higher, report repeats.

"""                                                     "Otherwise -r read method applies [default: 5]",0)


Clone Instance
30
Line Count
5
Source Line
104
Source File
Bio/Sequencing/Applications/_Novoalign.py

            _Option(["-e","recorded"],["input"],
                    lambda x:isinstance(x,types.IntType),0,"""Alignments recorded with score equal to the best.

"""                                                     "Default: 1000 in default read method, otherwise no limit.",0)


Clone Instance
31
Line Count
4
Source Line
109
Source File
Bio/Sequencing/Applications/_Novoalign.py

            _Option(["-q","qual_digits"],["input"],
                    lambda x:isinstance(x,types.IntType),0,"Decimal digits for quality scores [default: 0]",0)


Clone Instance
32
Line Count
4
Source Line
119
Source File
Bio/Sequencing/Applications/_Novoalign.py

            _Option(["-v","variation"],["input"],
                    lambda x:isinstance(x,types.IntType),0,"Structural variation penalty [default: 70]",0)


Clone Instance
33
Line Count
4
Source Line
125
Source File
Bio/Sequencing/Applications/_Novoalign.py

            # miRNA mode
            _Option(["-m","miRNA"],["input"],
                    lambda x:isinstance(x,types.IntType),0,"Sets miRNA mode and optionally sets a value for the region scanned [default: off]",0)


Clone Instance
34
Line Count
4
Source Line
131
Source File
Bio/Sequencing/Applications/_Novoalign.py

            # Multithreading
            _Option(["-c","cores"],["input"],
                    lambda x:isinstance(x,types.IntType),0,"Number of threads, disabled on free versions [default: number of cores]",0)


Clone Instance
35
Line Count
4
Source Line
137
Source File
Bio/Sequencing/Applications/_Novoalign.py

            # Quality calibrations
            _Option(["-k","read_cal"],["input"],
                    lambda x:isinstance(x,types.StringType),0,"Read quality calibration from file (mismatch counts)",0)


Clone Instance
36
Line Count
4
Source Line
141
Source File
Bio/Sequencing/Applications/_Novoalign.py

            _Option(["-K","write_cal"],["input"],
                    lambda x:isinstance(x,types.StringType),0,"Accumulate mismatch counts and write to file",0)


Clone AbstractionParameter Count: 4Parameter Bindings

#SUEFF           Floating point value 0.1                Constant used in UPGMB
#                between 0 and 1.                        clustering. Determines
#                                                        the relative fraction
#                                                        of average linkage
#                                                        (SUEFF) vs. nearest-
#                                                        neighbor linkage (1
#                                                        SUEFF).
#smoothwindow    Integer              7                  Window used for anchor
#                                                        column smoothing.
#smoothscoreceil Floating point       [1]                Maximum value of column
#                                                        score for smoothing
#                                                        purposes.
#minbestcolscore Floating point       [1]                Minimum score a column
#                                                        must have to be an
#                                                        anchor.
#maxtrees        Integer              1                  Maximum number of new
#                                                        trees to build in
#                                                        iteration 2.
#maxiters        Integer 1, 2 ...     16                 Maximum number of
#                                                        iterations.
#maxhours        Floating point       None.              Maximum time to run in
#                                                        hours. The actual time
#                                                        may exceed the
#                                                        requested limit by a
#                                                        few minutes. Decimals
#                                                        are allowed, so 1.5
#                                                        means one hour and 30
#                                                        minutes.
#hydrofactor     Floating point       1.2                Multiplier for gap
#                                                        open/close penalties in
#                                                        hydrophobic regions.
#hydro           Integer              5                  Window size for
#                                                        determining whether a
#                                                        region is hydrophobic.
#gapopen         Floating point       [1]                The gap open score.
#                                                        Must be negative.
#diagmargin      Integer              5                  Discard this many
#                                                        positions at ends of
#diaglength      Integer              24                 Minimum length of
#                                                        diagonal.
#center          Floating point       [1]                Center parameter.
#                                                        Should be negative.
#anchorspacing   Integer              32                 Minimum spacing between
# Quality calibrations
# Multithreading
# miRNA mode
# Read preprocessing options
# Quality control and read filtering
# Alignment scoring options
_Option([ [[#variable77adc0a0]], [[#variable77516860]]],["input"], lambda x:isinstance(x,types. [[#variable77adc040]]),0, [[#variable77516900]],0)
 

CloneAbstraction
Parameter Bindings
Parameter
Index
Clone
Instance
Parameter
Name
Value
11[[#77adc0a0]]
"-thr" 
12[[#77adc0a0]]
"-sueff" 
13[[#77adc0a0]]
"-smoothwindow" 
14[[#77adc0a0]]
"-smoothscoreceil" 
15[[#77adc0a0]]
"-minbestcolscore" 
16[[#77adc0a0]]
"-maxtrees" 
17[[#77adc0a0]]
"-maxiters" 
18[[#77adc0a0]]
"-maxhours" 
19[[#77adc0a0]]
"-hydrofactor" 
110[[#77adc0a0]]
"-hydro" 
111[[#77adc0a0]]
"-gapopen" 
112[[#77adc0a0]]
"-diagmargin" 
113[[#77adc0a0]]
"-diaglength" 
114[[#77adc0a0]]
"-center" 
115[[#77adc0a0]]
"-anchorspacing" 
116[[#77adc0a0]]
"-gapext" 
117[[#77adc0a0]]
"-gapopen" 
118[[#77adc0a0]]
"-K" 
119[[#77adc0a0]]
"-k" 
120[[#77adc0a0]]
"-c" 
121[[#77adc0a0]]
"-m" 
122[[#77adc0a0]]
"-v" 
123[[#77adc0a0]]
"-q" 
124[[#77adc0a0]]
"-e" 
125[[#77adc0a0]]
"-R" 
126[[#77adc0a0]]
"-Q" 
127[[#77adc0a0]]
"-5" 
128[[#77adc0a0]]
"-s" 
129[[#77adc0a0]]
"-n" 
130[[#77adc0a0]]
"-a" 
131[[#77adc0a0]]
"-h" 
132[[#77adc0a0]]
"-l" 
133[[#77adc0a0]]
"-u" 
134[[#77adc0a0]]
"-x" 
135[[#77adc0a0]]
"-g" 
136[[#77adc0a0]]
"-t" 
21[[#77516860]]
"thr" 
22[[#77516860]]
"sueff" 
23[[#77516860]]
"smoothwindow" 
24[[#77516860]]
"smoothscoreceil" 
25[[#77516860]]
"minbestcolscore" 
26[[#77516860]]
"maxtrees" 
27[[#77516860]]
"maxiters" 
28[[#77516860]]
"maxhours" 
29[[#77516860]]
"hydrofactor" 
210[[#77516860]]
"hydro" 
211[[#77516860]]
"gapopen" 
212[[#77516860]]
"diagmargin" 
213[[#77516860]]
"diaglength" 
214[[#77516860]]
"center" 
215[[#77516860]]
"anchorspacing" 
216[[#77516860]]
"gapext" 
217[[#77516860]]
"gapopen" 
218[[#77516860]]
"write_cal" 
219[[#77516860]]
"read_cal" 
220[[#77516860]]
"cores" 
221[[#77516860]]
"miRNA" 
222[[#77516860]]
"variation" 
223[[#77516860]]
"qual_digits" 
224[[#77516860]]
"recorded" 
225[[#77516860]]
"repeats" 
226[[#77516860]]
"quality" 
227[[#77516860]]
"adapter5" 
228[[#77516860]]
"trimming" 
229[[#77516860]]
"truncate" 
230[[#77516860]]
"adapter3" 
231[[#77516860]]
"homopolymer" 
232[[#77516860]]
"good_bases" 
233[[#77516860]]
"unconverted" 
234[[#77516860]]
"gap_extend" 
235[[#77516860]]
"gap_open" 
236[[#77516860]]
"threshold" 
31[[#77adc040]]
IntType 
32[[#77adc040]]
FloatType 
33[[#77adc040]]
IntType 
34[[#77adc040]]
FloatType 
35[[#77adc040]]
FloatType 
36[[#77adc040]]
IntType 
37[[#77adc040]]
IntType 
38[[#77adc040]]
FloatType 
39[[#77adc040]]
FloatType 
310[[#77adc040]]
IntType 
311[[#77adc040]]
FloatType 
312[[#77adc040]]
IntType 
313[[#77adc040]]
IntType 
314[[#77adc040]]
FloatType 
315[[#77adc040]]
IntType 
316[[#77adc040]]
IntType 
317[[#77adc040]]
IntType 
318[[#77adc040]]
StringType 
319[[#77adc040]]
StringType 
320[[#77adc040]]
IntType 
321[[#77adc040]]
IntType 
322[[#77adc040]]
IntType 
323[[#77adc040]]
IntType 
324[[#77adc040]]
IntType 
325[[#77adc040]]
IntType 
326[[#77adc040]]
IntType 
327[[#77adc040]]
StringType 
328[[#77adc040]]
IntType 
329[[#77adc040]]
IntType 
330[[#77adc040]]
StringType 
331[[#77adc040]]
IntType 
332[[#77adc040]]
IntType 
333[[#77adc040]]
IntType 
334[[#77adc040]]
IntType 
335[[#77adc040]]
IntType 
336[[#77adc040]]
IntType 
41[[#77516900]]
"Threshold T = x." 
42[[#77516900]]
"Constant used in UPGMB clustering" 
43[[#77516900]]
"Window used for anchor column smoothing" 
44[[#77516900]]
"Maximum value of column score for smoothing" 
45[[#77516900]]
"Minimum score a column must have to be an anchor" 
46[[#77516900]]
"Maximum number of trees to build in iteration 2" 
47[[#77516900]]
"Maximum number of iterations" 
48[[#77516900]]
"Maximum time to run in hours" 
49[[#77516900]]
"Multiplier for gap penalties in hydrophobic regions" 
410[[#77516900]]
"Window size for hydrophobic region" 
411[[#77516900]]
"Gap open score - negative number" 
412[[#77516900]]
"Discard this many positions at ends of diagonal" 
413[[#77516900]]
"Minimum length of diagonal" 
414[[#77516900]]
"Center parameter - should be negative" 
415[[#77516900]]
"Minimum spacing between anchor columns" 
416[[#77516900]]
"Indicates the penalty applied for extending a " "gap. (negative integer)" 
417[[#77516900]]
"Indicates the penalty applied for opening a gap " "(negative integer)" 
418[[#77516900]]
"Accumulate mismatch counts and write to file" 
419[[#77516900]]
"Read quality calibration from file (mismatch counts)" 
420[[#77516900]]
"Number of threads, disabled on free versions [default: number of cores]" 
421[[#77516900]]
"Sets miRNA mode and optionally sets a value for the region scanned [default: off]" 
422[[#77516900]]
"Structural variation penalty [default: 70]" 
423[[#77516900]]
"Decimal digits for quality scores [default: 0]" 
424[[#77516900]]
"""Alignments recorded with score equal to the best.

""" "Default: 1000 in default read method, otherwise no limit." 
425[[#77516900]]
"""If score difference is higher, report repeats.

""" "Otherwise -r read method applies [default: 5]" 
426[[#77516900]]
"Lower threshold for an alignment to be reported [default: 0]" 
427[[#77516900]]
"""Strips a 5' adapter sequence.

""" "Similar to -a (adaptor_3), but on the 5' end." 
428[[#77516900]]
"""If fail to align, trim by s bases until they map or become shorter than l.

""" "Ddefault: 2" 
429[[#77516900]]
"Truncate to specific length before alignment" 
430[[#77516900]]
"""Strips a 3' adapter sequence prior to alignment.

""" "With paired ends two adapters can be specified" 
431[[#77516900]]
"Homopolymer read filter [default: 20; disable: negative value]" 
432[[#77516900]]
"Minimum number of good quality bases [default: log(N_g, 4) + 5]" 
433[[#77516900]]
"""Experimental: unconverted cytosines penalty in bisulfite mode

""" "Default: no penalty" 
434[[#77516900]]
"Gap extend penalty [default: 15]" 
435[[#77516900]]
"Gap opening penalty [default: 40]" 
436[[#77516900]]
"Threshold for alignment score"