Bio.Emboss package
Submodules
- Bio.Emboss.Applications module
Primer3Commandline
Primer3Commandline.__init__()
Primer3Commandline.auto
Primer3Commandline.debug
Primer3Commandline.die
Primer3Commandline.dnaconc
Primer3Commandline.error
Primer3Commandline.excludedregion
Primer3Commandline.explainflag
Primer3Commandline.filter
Primer3Commandline.forwardinput
Primer3Commandline.gcclamp
Primer3Commandline.help
Primer3Commandline.hybridprobe
Primer3Commandline.includedregion
Primer3Commandline.maxdifftm
Primer3Commandline.maxgc
Primer3Commandline.maxmispriming
Primer3Commandline.maxpolyx
Primer3Commandline.maxsize
Primer3Commandline.maxtm
Primer3Commandline.mingc
Primer3Commandline.minsize
Primer3Commandline.mintm
Primer3Commandline.mishyblibraryfile
Primer3Commandline.mispriminglibraryfile
Primer3Commandline.numreturn
Primer3Commandline.oanyself
Primer3Commandline.odnaconc
Primer3Commandline.oendself
Primer3Commandline.oexcludedregion
Primer3Commandline.ogcmax
Primer3Commandline.ogcmin
Primer3Commandline.ogcopt
Primer3Commandline.ogcpercent
Primer3Commandline.oligoinput
Primer3Commandline.omaxsize
Primer3Commandline.ominsize
Primer3Commandline.omishybmax
Primer3Commandline.opolyxmax
Primer3Commandline.options
Primer3Commandline.opttm
Primer3Commandline.osaltconc
Primer3Commandline.osize
Primer3Commandline.osizeopt
Primer3Commandline.otm
Primer3Commandline.otmmax
Primer3Commandline.otmmin
Primer3Commandline.otmopt
Primer3Commandline.outfile
Primer3Commandline.prange
Primer3Commandline.psizeopt
Primer3Commandline.ptmmax
Primer3Commandline.ptmmin
Primer3Commandline.ptmopt
Primer3Commandline.reverseinput
Primer3Commandline.saltconc
Primer3Commandline.sequence
Primer3Commandline.stdout
Primer3Commandline.target
Primer3Commandline.task
Primer3Commandline.verbose
Primer3Commandline.warning
PrimerSearchCommandline
PrimerSearchCommandline.__init__()
PrimerSearchCommandline.auto
PrimerSearchCommandline.debug
PrimerSearchCommandline.die
PrimerSearchCommandline.error
PrimerSearchCommandline.filter
PrimerSearchCommandline.help
PrimerSearchCommandline.infile
PrimerSearchCommandline.mismatchpercent
PrimerSearchCommandline.options
PrimerSearchCommandline.outfile
PrimerSearchCommandline.seqall
PrimerSearchCommandline.snucleotide
PrimerSearchCommandline.sprotein
PrimerSearchCommandline.stdout
PrimerSearchCommandline.verbose
PrimerSearchCommandline.warning
FDNADistCommandline
FDNADistCommandline.__init__()
FDNADistCommandline.auto
FDNADistCommandline.basefreq
FDNADistCommandline.categories
FDNADistCommandline.debug
FDNADistCommandline.die
FDNADistCommandline.error
FDNADistCommandline.filter
FDNADistCommandline.freqsfrom
FDNADistCommandline.gamma
FDNADistCommandline.gammacoefficient
FDNADistCommandline.help
FDNADistCommandline.invarfrac
FDNADistCommandline.lower
FDNADistCommandline.method
FDNADistCommandline.ncategories
FDNADistCommandline.options
FDNADistCommandline.outfile
FDNADistCommandline.rate
FDNADistCommandline.sequence
FDNADistCommandline.stdout
FDNADistCommandline.ttratio
FDNADistCommandline.verbose
FDNADistCommandline.warning
FDNADistCommandline.weights
FTreeDistCommandline
FTreeDistCommandline.__init__()
FTreeDistCommandline.auto
FTreeDistCommandline.debug
FTreeDistCommandline.die
FTreeDistCommandline.dtype
FTreeDistCommandline.error
FTreeDistCommandline.filter
FTreeDistCommandline.help
FTreeDistCommandline.intreefile
FTreeDistCommandline.noroot
FTreeDistCommandline.options
FTreeDistCommandline.outfile
FTreeDistCommandline.outgrno
FTreeDistCommandline.pairing
FTreeDistCommandline.stdout
FTreeDistCommandline.style
FTreeDistCommandline.verbose
FTreeDistCommandline.warning
FNeighborCommandline
FNeighborCommandline.__init__()
FNeighborCommandline.auto
FNeighborCommandline.datafile
FNeighborCommandline.debug
FNeighborCommandline.die
FNeighborCommandline.error
FNeighborCommandline.filter
FNeighborCommandline.help
FNeighborCommandline.jumble
FNeighborCommandline.matrixtype
FNeighborCommandline.options
FNeighborCommandline.outfile
FNeighborCommandline.outgrno
FNeighborCommandline.outtreefile
FNeighborCommandline.progress
FNeighborCommandline.seed
FNeighborCommandline.stdout
FNeighborCommandline.treeprint
FNeighborCommandline.treetype
FNeighborCommandline.trout
FNeighborCommandline.verbose
FNeighborCommandline.warning
FSeqBootCommandline
FSeqBootCommandline.__init__()
FSeqBootCommandline.auto
FSeqBootCommandline.blocksize
FSeqBootCommandline.catergories
FSeqBootCommandline.debug
FSeqBootCommandline.die
FSeqBootCommandline.dotdiff
FSeqBootCommandline.error
FSeqBootCommandline.filter
FSeqBootCommandline.fracsample
FSeqBootCommandline.help
FSeqBootCommandline.jusweights
FSeqBootCommandline.options
FSeqBootCommandline.outfile
FSeqBootCommandline.regular
FSeqBootCommandline.reps
FSeqBootCommandline.rewriteformat
FSeqBootCommandline.seed
FSeqBootCommandline.seqtype
FSeqBootCommandline.sequence
FSeqBootCommandline.stdout
FSeqBootCommandline.test
FSeqBootCommandline.verbose
FSeqBootCommandline.warning
FSeqBootCommandline.weights
FDNAParsCommandline
FDNAParsCommandline.__init__()
FDNAParsCommandline.auto
FDNAParsCommandline.debug
FDNAParsCommandline.die
FDNAParsCommandline.dotdiff
FDNAParsCommandline.error
FDNAParsCommandline.filter
FDNAParsCommandline.help
FDNAParsCommandline.intreefile
FDNAParsCommandline.maxtrees
FDNAParsCommandline.njumble
FDNAParsCommandline.options
FDNAParsCommandline.outfile
FDNAParsCommandline.outgrno
FDNAParsCommandline.outtreefile
FDNAParsCommandline.rearrange
FDNAParsCommandline.seed
FDNAParsCommandline.sequence
FDNAParsCommandline.stdout
FDNAParsCommandline.thorough
FDNAParsCommandline.thresh
FDNAParsCommandline.threshold
FDNAParsCommandline.transversion
FDNAParsCommandline.trout
FDNAParsCommandline.verbose
FDNAParsCommandline.warning
FDNAParsCommandline.weights
FProtParsCommandline
FProtParsCommandline.__init__()
FProtParsCommandline.auto
FProtParsCommandline.debug
FProtParsCommandline.die
FProtParsCommandline.dotdiff
FProtParsCommandline.error
FProtParsCommandline.filter
FProtParsCommandline.help
FProtParsCommandline.intreefile
FProtParsCommandline.njumble
FProtParsCommandline.options
FProtParsCommandline.outfile
FProtParsCommandline.outgrno
FProtParsCommandline.outtreefile
FProtParsCommandline.seed
FProtParsCommandline.sequence
FProtParsCommandline.stdout
FProtParsCommandline.thresh
FProtParsCommandline.threshold
FProtParsCommandline.trout
FProtParsCommandline.verbose
FProtParsCommandline.warning
FProtParsCommandline.weights
FProtParsCommandline.whichcode
FProtDistCommandline
FProtDistCommandline.__init__()
FProtDistCommandline.aacateg
FProtDistCommandline.auto
FProtDistCommandline.basefreq
FProtDistCommandline.catergories
FProtDistCommandline.debug
FProtDistCommandline.die
FProtDistCommandline.ease
FProtDistCommandline.error
FProtDistCommandline.filter
FProtDistCommandline.gamma
FProtDistCommandline.gammacoefficient
FProtDistCommandline.help
FProtDistCommandline.invarcoefficient
FProtDistCommandline.method
FProtDistCommandline.ncategories
FProtDistCommandline.options
FProtDistCommandline.outfile
FProtDistCommandline.rate
FProtDistCommandline.sequence
FProtDistCommandline.stdout
FProtDistCommandline.ttratio
FProtDistCommandline.verbose
FProtDistCommandline.warning
FProtDistCommandline.weights
FProtDistCommandline.whichcode
FConsenseCommandline
FConsenseCommandline.__init__()
FConsenseCommandline.auto
FConsenseCommandline.debug
FConsenseCommandline.die
FConsenseCommandline.error
FConsenseCommandline.filter
FConsenseCommandline.help
FConsenseCommandline.intreefile
FConsenseCommandline.method
FConsenseCommandline.mlfrac
FConsenseCommandline.options
FConsenseCommandline.outfile
FConsenseCommandline.outgrno
FConsenseCommandline.outtreefile
FConsenseCommandline.root
FConsenseCommandline.stdout
FConsenseCommandline.trout
FConsenseCommandline.verbose
FConsenseCommandline.warning
WaterCommandline
WaterCommandline.__init__()
WaterCommandline.aformat
WaterCommandline.asequence
WaterCommandline.auto
WaterCommandline.brief
WaterCommandline.bsequence
WaterCommandline.datafile
WaterCommandline.debug
WaterCommandline.die
WaterCommandline.error
WaterCommandline.filter
WaterCommandline.gapextend
WaterCommandline.gapopen
WaterCommandline.help
WaterCommandline.nobrief
WaterCommandline.options
WaterCommandline.outfile
WaterCommandline.similarity
WaterCommandline.snucleotide
WaterCommandline.sprotein
WaterCommandline.stdout
WaterCommandline.verbose
WaterCommandline.warning
NeedleCommandline
NeedleCommandline.__init__()
NeedleCommandline.aformat
NeedleCommandline.asequence
NeedleCommandline.auto
NeedleCommandline.brief
NeedleCommandline.bsequence
NeedleCommandline.datafile
NeedleCommandline.debug
NeedleCommandline.die
NeedleCommandline.endextend
NeedleCommandline.endopen
NeedleCommandline.endweight
NeedleCommandline.error
NeedleCommandline.filter
NeedleCommandline.gapextend
NeedleCommandline.gapopen
NeedleCommandline.help
NeedleCommandline.nobrief
NeedleCommandline.options
NeedleCommandline.outfile
NeedleCommandline.similarity
NeedleCommandline.snucleotide
NeedleCommandline.sprotein
NeedleCommandline.stdout
NeedleCommandline.verbose
NeedleCommandline.warning
NeedleallCommandline
NeedleallCommandline.__init__()
NeedleallCommandline.aformat
NeedleallCommandline.asequence
NeedleallCommandline.auto
NeedleallCommandline.brief
NeedleallCommandline.bsequence
NeedleallCommandline.datafile
NeedleallCommandline.debug
NeedleallCommandline.die
NeedleallCommandline.endextend
NeedleallCommandline.endopen
NeedleallCommandline.endweight
NeedleallCommandline.error
NeedleallCommandline.errorfile
NeedleallCommandline.filter
NeedleallCommandline.gapextend
NeedleallCommandline.gapopen
NeedleallCommandline.help
NeedleallCommandline.minscore
NeedleallCommandline.nobrief
NeedleallCommandline.options
NeedleallCommandline.outfile
NeedleallCommandline.similarity
NeedleallCommandline.snucleotide
NeedleallCommandline.sprotein
NeedleallCommandline.stdout
NeedleallCommandline.verbose
NeedleallCommandline.warning
StretcherCommandline
StretcherCommandline.__init__()
StretcherCommandline.aformat
StretcherCommandline.asequence
StretcherCommandline.auto
StretcherCommandline.bsequence
StretcherCommandline.datafile
StretcherCommandline.debug
StretcherCommandline.die
StretcherCommandline.error
StretcherCommandline.filter
StretcherCommandline.gapextend
StretcherCommandline.gapopen
StretcherCommandline.help
StretcherCommandline.options
StretcherCommandline.outfile
StretcherCommandline.snucleotide
StretcherCommandline.sprotein
StretcherCommandline.stdout
StretcherCommandline.verbose
StretcherCommandline.warning
FuzznucCommandline
FuzznucCommandline.__init__()
FuzznucCommandline.auto
FuzznucCommandline.complement
FuzznucCommandline.debug
FuzznucCommandline.die
FuzznucCommandline.error
FuzznucCommandline.filter
FuzznucCommandline.help
FuzznucCommandline.options
FuzznucCommandline.outfile
FuzznucCommandline.pattern
FuzznucCommandline.pmismatch
FuzznucCommandline.rformat
FuzznucCommandline.sequence
FuzznucCommandline.stdout
FuzznucCommandline.verbose
FuzznucCommandline.warning
FuzzproCommandline
FuzzproCommandline.__init__()
FuzzproCommandline.auto
FuzzproCommandline.debug
FuzzproCommandline.die
FuzzproCommandline.error
FuzzproCommandline.filter
FuzzproCommandline.help
FuzzproCommandline.options
FuzzproCommandline.outfile
FuzzproCommandline.pattern
FuzzproCommandline.pmismatch
FuzzproCommandline.rformat
FuzzproCommandline.sequence
FuzzproCommandline.stdout
FuzzproCommandline.verbose
FuzzproCommandline.warning
Est2GenomeCommandline
Est2GenomeCommandline.__init__()
Est2GenomeCommandline.align
Est2GenomeCommandline.auto
Est2GenomeCommandline.best
Est2GenomeCommandline.debug
Est2GenomeCommandline.die
Est2GenomeCommandline.error
Est2GenomeCommandline.est
Est2GenomeCommandline.filter
Est2GenomeCommandline.gappenalty
Est2GenomeCommandline.genome
Est2GenomeCommandline.help
Est2GenomeCommandline.intronpenalty
Est2GenomeCommandline.match
Est2GenomeCommandline.minscore
Est2GenomeCommandline.mismatch
Est2GenomeCommandline.mode
Est2GenomeCommandline.options
Est2GenomeCommandline.outfile
Est2GenomeCommandline.reverse
Est2GenomeCommandline.seed
Est2GenomeCommandline.shuffle
Est2GenomeCommandline.space
Est2GenomeCommandline.splice
Est2GenomeCommandline.splicepenalty
Est2GenomeCommandline.stdout
Est2GenomeCommandline.verbose
Est2GenomeCommandline.warning
Est2GenomeCommandline.width
ETandemCommandline
ETandemCommandline.__init__()
ETandemCommandline.auto
ETandemCommandline.debug
ETandemCommandline.die
ETandemCommandline.error
ETandemCommandline.filter
ETandemCommandline.help
ETandemCommandline.maxrepeat
ETandemCommandline.minrepeat
ETandemCommandline.mismatch
ETandemCommandline.options
ETandemCommandline.outfile
ETandemCommandline.rformat
ETandemCommandline.sequence
ETandemCommandline.stdout
ETandemCommandline.threshold
ETandemCommandline.uniform
ETandemCommandline.verbose
ETandemCommandline.warning
EInvertedCommandline
EInvertedCommandline.__init__()
EInvertedCommandline.auto
EInvertedCommandline.debug
EInvertedCommandline.die
EInvertedCommandline.error
EInvertedCommandline.filter
EInvertedCommandline.gap
EInvertedCommandline.help
EInvertedCommandline.match
EInvertedCommandline.maxrepeat
EInvertedCommandline.mismatch
EInvertedCommandline.options
EInvertedCommandline.outfile
EInvertedCommandline.sequence
EInvertedCommandline.stdout
EInvertedCommandline.threshold
EInvertedCommandline.verbose
EInvertedCommandline.warning
PalindromeCommandline
PalindromeCommandline.__init__()
PalindromeCommandline.auto
PalindromeCommandline.debug
PalindromeCommandline.die
PalindromeCommandline.error
PalindromeCommandline.filter
PalindromeCommandline.gaplimit
PalindromeCommandline.help
PalindromeCommandline.maxpallen
PalindromeCommandline.minpallen
PalindromeCommandline.nummismatches
PalindromeCommandline.options
PalindromeCommandline.outfile
PalindromeCommandline.overlap
PalindromeCommandline.sequence
PalindromeCommandline.stdout
PalindromeCommandline.verbose
PalindromeCommandline.warning
TranalignCommandline
TranalignCommandline.__init__()
TranalignCommandline.asequence
TranalignCommandline.auto
TranalignCommandline.bsequence
TranalignCommandline.debug
TranalignCommandline.die
TranalignCommandline.error
TranalignCommandline.filter
TranalignCommandline.help
TranalignCommandline.options
TranalignCommandline.outfile
TranalignCommandline.outseq
TranalignCommandline.stdout
TranalignCommandline.table
TranalignCommandline.verbose
TranalignCommandline.warning
DiffseqCommandline
DiffseqCommandline.__init__()
DiffseqCommandline.aoutfeat
DiffseqCommandline.asequence
DiffseqCommandline.auto
DiffseqCommandline.boutfeat
DiffseqCommandline.bsequence
DiffseqCommandline.debug
DiffseqCommandline.die
DiffseqCommandline.error
DiffseqCommandline.filter
DiffseqCommandline.help
DiffseqCommandline.options
DiffseqCommandline.outfile
DiffseqCommandline.rformat
DiffseqCommandline.stdout
DiffseqCommandline.verbose
DiffseqCommandline.warning
DiffseqCommandline.wordsize
IepCommandline
IepCommandline.__init__()
IepCommandline.amino
IepCommandline.auto
IepCommandline.carboxyl
IepCommandline.debug
IepCommandline.die
IepCommandline.disulphides
IepCommandline.error
IepCommandline.filter
IepCommandline.help
IepCommandline.lysinemodified
IepCommandline.notermini
IepCommandline.options
IepCommandline.outfile
IepCommandline.sequence
IepCommandline.stdout
IepCommandline.verbose
IepCommandline.warning
SeqretCommandline
SeqretCommandline.__init__()
SeqretCommandline.auto
SeqretCommandline.debug
SeqretCommandline.die
SeqretCommandline.error
SeqretCommandline.filter
SeqretCommandline.help
SeqretCommandline.options
SeqretCommandline.osformat
SeqretCommandline.outseq
SeqretCommandline.sequence
SeqretCommandline.sformat
SeqretCommandline.stdout
SeqretCommandline.verbose
SeqretCommandline.warning
SeqmatchallCommandline
SeqmatchallCommandline.__init__()
SeqmatchallCommandline.aformat
SeqmatchallCommandline.auto
SeqmatchallCommandline.debug
SeqmatchallCommandline.die
SeqmatchallCommandline.error
SeqmatchallCommandline.filter
SeqmatchallCommandline.help
SeqmatchallCommandline.options
SeqmatchallCommandline.outfile
SeqmatchallCommandline.sequence
SeqmatchallCommandline.stdout
SeqmatchallCommandline.verbose
SeqmatchallCommandline.warning
SeqmatchallCommandline.wordsize
- Bio.Emboss.Primer3 module
- Bio.Emboss.PrimerSearch module
Module contents
Code to interact with the ever-so-useful EMBOSS programs.