CloneSet11

Bio/Align/Applications/_Dialign.py

Bio/Align/Applications/_Muscle.py

Bio/Align/Applications/_Muscle.py

Bio/Align/Applications/_Muscle.py

Bio/Align/Applications/_Muscle.py

Bio/Align/Applications/_Muscle.py

Bio/Align/Applications/_Muscle.py

Bio/Align/Applications/_Muscle.py

Bio/Align/Applications/_Muscle.py

Bio/Align/Applications/_Muscle.py

Bio/Align/Applications/_Muscle.py

Bio/Align/Applications/_Muscle.py

Bio/Align/Applications/_Muscle.py

Bio/Align/Applications/_Muscle.py

Bio/Align/Applications/_Muscle.py

Bio/Align/Applications/_TCoffee.py

Bio/Align/Applications/_TCoffee.py

Bio/Sequencing/Applications/_Novoalign.py

Bio/Sequencing/Applications/_Novoalign.py

Bio/Sequencing/Applications/_Novoalign.py

Bio/Sequencing/Applications/_Novoalign.py

Bio/Sequencing/Applications/_Novoalign.py

Bio/Sequencing/Applications/_Novoalign.py

Bio/Sequencing/Applications/_Novoalign.py

Bio/Sequencing/Applications/_Novoalign.py

Bio/Sequencing/Applications/_Novoalign.py

Bio/Sequencing/Applications/_Novoalign.py

Bio/Sequencing/Applications/_Novoalign.py

Bio/Sequencing/Applications/_Novoalign.py

Bio/Sequencing/Applications/_Novoalign.py

Bio/Sequencing/Applications/_Novoalign.py

Bio/Sequencing/Applications/_Novoalign.py

Bio/Sequencing/Applications/_Novoalign.py

Bio/Sequencing/Applications/_Novoalign.py

Bio/Sequencing/Applications/_Novoalign.py

Bio/Sequencing/Applications/_Novoalign.py

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

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

            #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)

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

            #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)

            #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)

            #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)

            #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)

            #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)

            #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)

            #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)

            #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)

            #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)

            #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)

            #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)

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

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

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

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

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

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

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

            # 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)

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

            # 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)

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

            _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)

            _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)

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

            _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)

            _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)

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

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

            # 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)

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

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

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

#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)
 

"-thr" 

"-sueff" 

"-smoothwindow" 

"-smoothscoreceil" 

"-minbestcolscore" 

"-maxtrees" 

"-maxiters" 

"-maxhours" 

"-hydrofactor" 

"-hydro" 

"-gapopen" 

"-diagmargin" 

"-diaglength" 

"-center" 

"-anchorspacing" 

"-gapext" 

"-gapopen" 

"-K" 

"-k" 

"-c" 

"-m" 

"-v" 

"-q" 

"-e" 

"-R" 

"-Q" 

"-5" 

"-s" 

"-n" 

"-a" 

"-h" 

"-l" 

"-u" 

"-x" 

"-g" 

"-t" 

"thr" 

"sueff" 

"smoothwindow" 

"smoothscoreceil" 

"minbestcolscore" 

"maxtrees" 

"maxiters" 

"maxhours" 

"hydrofactor" 

"hydro" 

"gapopen" 

"diagmargin" 

"diaglength" 

"center" 

"anchorspacing" 

"gapext" 

"gapopen" 

"write_cal" 

"read_cal" 

"cores" 

"miRNA" 

"variation" 

"qual_digits" 

"recorded" 

"repeats" 

"quality" 

"adapter5" 

"trimming" 

"truncate" 

"adapter3" 

"homopolymer" 

"good_bases" 

"unconverted" 

"gap_extend" 

"gap_open" 

"threshold" 

IntType 

FloatType 

IntType 

FloatType 

FloatType 

IntType 

IntType 

FloatType 

FloatType 

IntType 

FloatType 

IntType 

IntType 

FloatType 

IntType 

IntType 

IntType 

StringType 

StringType 

IntType 

IntType 

IntType 

IntType 

IntType 

IntType 

IntType 

StringType 

IntType 

IntType 

StringType 

IntType 

IntType 

IntType 

IntType 

IntType 

IntType 

"Threshold T = x." 

"Constant used in UPGMB clustering" 

"Window used for anchor column smoothing" 

"Maximum value of column score for smoothing" 

"Minimum score a column must have to be an anchor" 

"Maximum number of trees to build in iteration 2" 

"Maximum number of iterations" 

"Maximum time to run in hours" 

"Multiplier for gap penalties in hydrophobic regions" 

"Window size for hydrophobic region" 

"Gap open score - negative number" 

"Discard this many positions at ends of diagonal" 

"Minimum length of diagonal" 

"Center parameter - should be negative" 

"Minimum spacing between anchor columns" 

"Indicates the penalty applied for extending a " "gap. (negative integer)" 

"Indicates the penalty applied for opening a gap " "(negative integer)" 

"Accumulate mismatch counts and write to file" 

"Read quality calibration from file (mismatch counts)" 

"Number of threads, disabled on free versions [default: number of cores]" 

"Sets miRNA mode and optionally sets a value for the region scanned [default: off]" 

"Structural variation penalty [default: 70]" 

"Decimal digits for quality scores [default: 0]" 

"""Alignments recorded with score equal to the best.

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

"""If score difference is higher, report repeats.

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

"Lower threshold for an alignment to be reported [default: 0]" 

"""Strips a 5' adapter sequence.

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

"""If fail to align, trim by s bases until they map or become shorter than l.

""" "Ddefault: 2" 

"Truncate to specific length before alignment" 

"""Strips a 3' adapter sequence prior to alignment.

""" "With paired ends two adapters can be specified" 

"Homopolymer read filter [default: 20; disable: negative value]" 

"Minimum number of good quality bases [default: log(N_g, 4) + 5]" 

"""Experimental: unconverted cytosines penalty in bisulfite mode

""" "Default: no penalty" 

"Gap extend penalty [default: 15]" 

"Gap opening penalty [default: 40]" 

"Threshold for alignment score"