Previous CloneSet | Next CloneSet | Back to Main Report |
Clone Mass | Clones in CloneSet | Parameter Count | Clone Similarity | Syntax Category [Sequence Length] |
---|---|---|---|---|
5 | 36 | 4 | 0.962 | or_test |
Clone Abstraction | Parameter Bindings |
Clone Instance (Click to see clone) | Line Count | Source Line | Source File |
---|---|---|---|
1 | 5 | 160 | Bio/Align/Applications/_Dialign.py |
2 | 5 | 57 | Bio/Align/Applications/_Muscle.py |
3 | 5 | 64 | Bio/Align/Applications/_Muscle.py |
4 | 5 | 84 | Bio/Align/Applications/_Muscle.py |
5 | 5 | 92 | Bio/Align/Applications/_Muscle.py |
6 | 5 | 120 | Bio/Align/Applications/_Muscle.py |
7 | 5 | 128 | Bio/Align/Applications/_Muscle.py |
8 | 5 | 136 | Bio/Align/Applications/_Muscle.py |
9 | 5 | 172 | Bio/Align/Applications/_Muscle.py |
10 | 5 | 179 | Bio/Align/Applications/_Muscle.py |
11 | 5 | 187 | Bio/Align/Applications/_Muscle.py |
12 | 5 | 195 | Bio/Align/Applications/_Muscle.py |
13 | 5 | 253 | Bio/Align/Applications/_Muscle.py |
14 | 5 | 260 | Bio/Align/Applications/_Muscle.py |
15 | 5 | 272 | Bio/Align/Applications/_Muscle.py |
16 | 6 | 68 | Bio/Align/Applications/_TCoffee.py |
17 | 6 | 74 | Bio/Align/Applications/_TCoffee.py |
18 | 4 | 34 | Bio/Sequencing/Applications/_Novoalign.py |
19 | 4 | 38 | Bio/Sequencing/Applications/_Novoalign.py |
20 | 4 | 42 | Bio/Sequencing/Applications/_Novoalign.py |
21 | 5 | 46 | Bio/Sequencing/Applications/_Novoalign.py |
22 | 4 | 53 | Bio/Sequencing/Applications/_Novoalign.py |
23 | 4 | 57 | Bio/Sequencing/Applications/_Novoalign.py |
24 | 5 | 63 | Bio/Sequencing/Applications/_Novoalign.py |
25 | 4 | 68 | Bio/Sequencing/Applications/_Novoalign.py |
26 | 5 | 72 | Bio/Sequencing/Applications/_Novoalign.py |
27 | 5 | 77 | Bio/Sequencing/Applications/_Novoalign.py |
28 | 4 | 88 | Bio/Sequencing/Applications/_Novoalign.py |
29 | 5 | 92 | Bio/Sequencing/Applications/_Novoalign.py |
30 | 5 | 104 | Bio/Sequencing/Applications/_Novoalign.py |
31 | 4 | 109 | Bio/Sequencing/Applications/_Novoalign.py |
32 | 4 | 119 | Bio/Sequencing/Applications/_Novoalign.py |
33 | 4 | 125 | Bio/Sequencing/Applications/_Novoalign.py |
34 | 4 | 131 | Bio/Sequencing/Applications/_Novoalign.py |
35 | 4 | 137 | Bio/Sequencing/Applications/_Novoalign.py |
36 | 4 | 141 | Bio/Sequencing/Applications/_Novoalign.py |
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_Option(["-thr","thr"],["input"], lambda x:isinstance(x,types.IntType),0,"Threshold T = x.",0) |
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#anchorspacing Integer 32 Minimum spacing between _Option(["-anchorspacing","anchorspacing"],["input"], lambda x:isinstance(x,types.IntType),0,"Minimum spacing between anchor columns",0) |
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#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) |
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#diaglength Integer 24 Minimum length of # diagonal. _Option(["-diaglength","diaglength"],["input"], lambda x:isinstance(x,types.IntType),0,"Minimum length of diagonal",0) |
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#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) |
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#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) |
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#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) |
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#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) |
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#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) |
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#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) |
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#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) |
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#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) |
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#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) |
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#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) |
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#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) |
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_Option(["-gapopen","gapopen"],["input"], lambda x:isinstance(x,types.IntType),0,"Indicates the penalty applied for opening a gap " "(negative integer)",0) |
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_Option(["-gapext","gapext"],["input"], lambda x:isinstance(x,types.IntType),0,"Indicates the penalty applied for extending a " "gap. (negative integer)",0) |
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# Alignment scoring options _Option(["-t","threshold"],["input"], lambda x:isinstance(x,types.IntType),0,"Threshold for alignment score",0) |
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_Option(["-g","gap_open"],["input"], lambda x:isinstance(x,types.IntType),0,"Gap opening penalty [default: 40]",0) |
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_Option(["-x","gap_extend"],["input"], lambda x:isinstance(x,types.IntType),0,"Gap extend penalty [default: 15]",0) |
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_Option(["-u","unconverted"],["input"], lambda x:isinstance(x,types.IntType),0,"""Experimental: unconverted cytosines penalty in bisulfite mode """ "Default: no penalty",0) |
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# 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) |
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_Option(["-h","homopolymer"],["input"], lambda x:isinstance(x,types.IntType),0,"Homopolymer read filter [default: 20; disable: negative value]",0) |
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# 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) |
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_Option(["-n","truncate"],["input"], lambda x:isinstance(x,types.IntType),0,"Truncate to specific length before alignment",0) |
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_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) |
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_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) |
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_Option(["-Q","quality"],["input"], lambda x:isinstance(x,types.IntType),0,"Lower threshold for an alignment to be reported [default: 0]",0) |
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_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) |
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_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) |
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_Option(["-q","qual_digits"],["input"], lambda x:isinstance(x,types.IntType),0,"Decimal digits for quality scores [default: 0]",0) |
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_Option(["-v","variation"],["input"], lambda x:isinstance(x,types.IntType),0,"Structural variation penalty [default: 70]",0) |
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# 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) |
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# Multithreading _Option(["-c","cores"],["input"], lambda x:isinstance(x,types.IntType),0,"Number of threads, disabled on free versions [default: number of cores]",0) |
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# Quality calibrations _Option(["-k","read_cal"],["input"], lambda x:isinstance(x,types.StringType),0,"Read quality calibration from file (mismatch counts)",0) |
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_Option(["-K","write_cal"],["input"], lambda x:isinstance(x,types.StringType),0,"Accumulate mismatch counts and write to file",0) |
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#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 Index | Clone Instance | Parameter Name | Value |
---|---|---|---|
1 | 1 | [[#77adc0a0]] | "-thr" |
1 | 2 | [[#77adc0a0]] | "-sueff" |
1 | 3 | [[#77adc0a0]] | "-smoothwindow" |
1 | 4 | [[#77adc0a0]] | "-smoothscoreceil" |
1 | 5 | [[#77adc0a0]] | "-minbestcolscore" |
1 | 6 | [[#77adc0a0]] | "-maxtrees" |
1 | 7 | [[#77adc0a0]] | "-maxiters" |
1 | 8 | [[#77adc0a0]] | "-maxhours" |
1 | 9 | [[#77adc0a0]] | "-hydrofactor" |
1 | 10 | [[#77adc0a0]] | "-hydro" |
1 | 11 | [[#77adc0a0]] | "-gapopen" |
1 | 12 | [[#77adc0a0]] | "-diagmargin" |
1 | 13 | [[#77adc0a0]] | "-diaglength" |
1 | 14 | [[#77adc0a0]] | "-center" |
1 | 15 | [[#77adc0a0]] | "-anchorspacing" |
1 | 16 | [[#77adc0a0]] | "-gapext" |
1 | 17 | [[#77adc0a0]] | "-gapopen" |
1 | 18 | [[#77adc0a0]] | "-K" |
1 | 19 | [[#77adc0a0]] | "-k" |
1 | 20 | [[#77adc0a0]] | "-c" |
1 | 21 | [[#77adc0a0]] | "-m" |
1 | 22 | [[#77adc0a0]] | "-v" |
1 | 23 | [[#77adc0a0]] | "-q" |
1 | 24 | [[#77adc0a0]] | "-e" |
1 | 25 | [[#77adc0a0]] | "-R" |
1 | 26 | [[#77adc0a0]] | "-Q" |
1 | 27 | [[#77adc0a0]] | "-5" |
1 | 28 | [[#77adc0a0]] | "-s" |
1 | 29 | [[#77adc0a0]] | "-n" |
1 | 30 | [[#77adc0a0]] | "-a" |
1 | 31 | [[#77adc0a0]] | "-h" |
1 | 32 | [[#77adc0a0]] | "-l" |
1 | 33 | [[#77adc0a0]] | "-u" |
1 | 34 | [[#77adc0a0]] | "-x" |
1 | 35 | [[#77adc0a0]] | "-g" |
1 | 36 | [[#77adc0a0]] | "-t" |
2 | 1 | [[#77516860]] | "thr" |
2 | 2 | [[#77516860]] | "sueff" |
2 | 3 | [[#77516860]] | "smoothwindow" |
2 | 4 | [[#77516860]] | "smoothscoreceil" |
2 | 5 | [[#77516860]] | "minbestcolscore" |
2 | 6 | [[#77516860]] | "maxtrees" |
2 | 7 | [[#77516860]] | "maxiters" |
2 | 8 | [[#77516860]] | "maxhours" |
2 | 9 | [[#77516860]] | "hydrofactor" |
2 | 10 | [[#77516860]] | "hydro" |
2 | 11 | [[#77516860]] | "gapopen" |
2 | 12 | [[#77516860]] | "diagmargin" |
2 | 13 | [[#77516860]] | "diaglength" |
2 | 14 | [[#77516860]] | "center" |
2 | 15 | [[#77516860]] | "anchorspacing" |
2 | 16 | [[#77516860]] | "gapext" |
2 | 17 | [[#77516860]] | "gapopen" |
2 | 18 | [[#77516860]] | "write_cal" |
2 | 19 | [[#77516860]] | "read_cal" |
2 | 20 | [[#77516860]] | "cores" |
2 | 21 | [[#77516860]] | "miRNA" |
2 | 22 | [[#77516860]] | "variation" |
2 | 23 | [[#77516860]] | "qual_digits" |
2 | 24 | [[#77516860]] | "recorded" |
2 | 25 | [[#77516860]] | "repeats" |
2 | 26 | [[#77516860]] | "quality" |
2 | 27 | [[#77516860]] | "adapter5" |
2 | 28 | [[#77516860]] | "trimming" |
2 | 29 | [[#77516860]] | "truncate" |
2 | 30 | [[#77516860]] | "adapter3" |
2 | 31 | [[#77516860]] | "homopolymer" |
2 | 32 | [[#77516860]] | "good_bases" |
2 | 33 | [[#77516860]] | "unconverted" |
2 | 34 | [[#77516860]] | "gap_extend" |
2 | 35 | [[#77516860]] | "gap_open" |
2 | 36 | [[#77516860]] | "threshold" |
3 | 1 | [[#77adc040]] | IntType |
3 | 2 | [[#77adc040]] | FloatType |
3 | 3 | [[#77adc040]] | IntType |
3 | 4 | [[#77adc040]] | FloatType |
3 | 5 | [[#77adc040]] | FloatType |
3 | 6 | [[#77adc040]] | IntType |
3 | 7 | [[#77adc040]] | IntType |
3 | 8 | [[#77adc040]] | FloatType |
3 | 9 | [[#77adc040]] | FloatType |
3 | 10 | [[#77adc040]] | IntType |
3 | 11 | [[#77adc040]] | FloatType |
3 | 12 | [[#77adc040]] | IntType |
3 | 13 | [[#77adc040]] | IntType |
3 | 14 | [[#77adc040]] | FloatType |
3 | 15 | [[#77adc040]] | IntType |
3 | 16 | [[#77adc040]] | IntType |
3 | 17 | [[#77adc040]] | IntType |
3 | 18 | [[#77adc040]] | StringType |
3 | 19 | [[#77adc040]] | StringType |
3 | 20 | [[#77adc040]] | IntType |
3 | 21 | [[#77adc040]] | IntType |
3 | 22 | [[#77adc040]] | IntType |
3 | 23 | [[#77adc040]] | IntType |
3 | 24 | [[#77adc040]] | IntType |
3 | 25 | [[#77adc040]] | IntType |
3 | 26 | [[#77adc040]] | IntType |
3 | 27 | [[#77adc040]] | StringType |
3 | 28 | [[#77adc040]] | IntType |
3 | 29 | [[#77adc040]] | IntType |
3 | 30 | [[#77adc040]] | StringType |
3 | 31 | [[#77adc040]] | IntType |
3 | 32 | [[#77adc040]] | IntType |
3 | 33 | [[#77adc040]] | IntType |
3 | 34 | [[#77adc040]] | IntType |
3 | 35 | [[#77adc040]] | IntType |
3 | 36 | [[#77adc040]] | IntType |
4 | 1 | [[#77516900]] | "Threshold T = x." |
4 | 2 | [[#77516900]] | "Constant used in UPGMB clustering" |
4 | 3 | [[#77516900]] | "Window used for anchor column smoothing" |
4 | 4 | [[#77516900]] | "Maximum value of column score for smoothing" |
4 | 5 | [[#77516900]] | "Minimum score a column must have to be an anchor" |
4 | 6 | [[#77516900]] | "Maximum number of trees to build in iteration 2" |
4 | 7 | [[#77516900]] | "Maximum number of iterations" |
4 | 8 | [[#77516900]] | "Maximum time to run in hours" |
4 | 9 | [[#77516900]] | "Multiplier for gap penalties in hydrophobic regions" |
4 | 10 | [[#77516900]] | "Window size for hydrophobic region" |
4 | 11 | [[#77516900]] | "Gap open score - negative number" |
4 | 12 | [[#77516900]] | "Discard this many positions at ends of diagonal" |
4 | 13 | [[#77516900]] | "Minimum length of diagonal" |
4 | 14 | [[#77516900]] | "Center parameter - should be negative" |
4 | 15 | [[#77516900]] | "Minimum spacing between anchor columns" |
4 | 16 | [[#77516900]] | "Indicates the penalty applied for extending a " "gap. (negative integer)" |
4 | 17 | [[#77516900]] | "Indicates the penalty applied for opening a gap " "(negative integer)" |
4 | 18 | [[#77516900]] | "Accumulate mismatch counts and write to file" |
4 | 19 | [[#77516900]] | "Read quality calibration from file (mismatch counts)" |
4 | 20 | [[#77516900]] | "Number of threads, disabled on free versions [default: number of cores]" |
4 | 21 | [[#77516900]] | "Sets miRNA mode and optionally sets a value for the region scanned [default: off]" |
4 | 22 | [[#77516900]] | "Structural variation penalty [default: 70]" |
4 | 23 | [[#77516900]] | "Decimal digits for quality scores [default: 0]" |
4 | 24 | [[#77516900]] | """Alignments recorded with score equal to the best. """ "Default: 1000 in default read method, otherwise no limit." |
4 | 25 | [[#77516900]] | """If score difference is higher, report repeats. """ "Otherwise -r read method applies [default: 5]" |
4 | 26 | [[#77516900]] | "Lower threshold for an alignment to be reported [default: 0]" |
4 | 27 | [[#77516900]] | """Strips a 5' adapter sequence. """ "Similar to -a (adaptor_3), but on the 5' end." |
4 | 28 | [[#77516900]] | """If fail to align, trim by s bases until they map or become shorter than l. """ "Ddefault: 2" |
4 | 29 | [[#77516900]] | "Truncate to specific length before alignment" |
4 | 30 | [[#77516900]] | """Strips a 3' adapter sequence prior to alignment. """ "With paired ends two adapters can be specified" |
4 | 31 | [[#77516900]] | "Homopolymer read filter [default: 20; disable: negative value]" |
4 | 32 | [[#77516900]] | "Minimum number of good quality bases [default: log(N_g, 4) + 5]" |
4 | 33 | [[#77516900]] | """Experimental: unconverted cytosines penalty in bisulfite mode """ "Default: no penalty" |
4 | 34 | [[#77516900]] | "Gap extend penalty [default: 15]" |
4 | 35 | [[#77516900]] | "Gap opening penalty [default: 40]" |
4 | 36 | [[#77516900]] | "Threshold for alignment score" |