Bio.Emboss.Applications module

Code to interact with and run various EMBOSS programs.

These classes follow the AbstractCommandline interfaces for running programs.

class Bio.Emboss.Applications.Primer3Commandline(cmd='eprimer3', **kwargs)

Bases: Bio.Emboss.Applications._EmbossCommandLine

Commandline object for the Primer3 interface from EMBOSS.

The precise set of supported arguments depends on your version of EMBOSS. This version accepts arguments current at EMBOSS 6.1.0, but in order to remain backwards compatible also support the old argument names as well.

e.g. Using EMBOSS 6.1.0 or later,

>>> cline = Primer3Commandline(sequence="mysequence.fas", auto=True, hybridprobe=True)
>>> cline.explainflag = True
>>> cline.osizeopt=20
>>> cline.psizeopt=200
>>> cline.outfile = "myresults.out"
>>> cline.bogusparameter = 1967     # Invalid parameter
Traceback (most recent call last):
    ...
ValueError: Option name bogusparameter was not found.
>>> print(cline)
eprimer3 -auto -outfile=myresults.out -sequence=mysequence.fas -hybridprobe=True -psizeopt=200 -osizeopt=20 -explainflag=True

The equivalent for anyone still using an older version of EMBOSS would be:

>>> cline = Primer3Commandline(sequence="mysequence.fas", auto=True, hybridprobe=True)
>>> cline.explainflag = True
>>> cline.oligosize=20              # Old EMBOSS, instead of osizeopt
>>> cline.productosize=200          # Old EMBOSS, instead of psizeopt
>>> cline.outfile = "myresults.out"
>>> print(cline)
eprimer3 -auto -outfile=myresults.out -sequence=mysequence.fas -hybridprobe=True -productosize=200 -oligosize=20 -explainflag=True

__init__(self, cmd='eprimer3', **kwargs)

Initialize the class.

property auto

Turn off prompts.

Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

This property controls the addition of the -auto switch, treat this property as a boolean.

property debug

Write debug output to program.dbg.

This property controls the addition of the -debug switch, treat this property as a boolean.

property die

Report dying program messages.

This property controls the addition of the -die switch, treat this property as a boolean.

property dnaconc

Nanomolar concentration of annealing oligos in the PCR.

This controls the addition of the -dnaconc parameter and its associated value. Set this property to the argument value required.

property error

Report errors.

This property controls the addition of the -error switch, treat this property as a boolean.

property excludedregion

Regions to exclude from primer picking.

This controls the addition of the -excludedregion parameter and its associated value. Set this property to the argument value required.

property explainflag

Produce output tags with eprimer3 statistics

This controls the addition of the -explainflag parameter and its associated value. Set this property to the argument value required.

property filter

Read standard input, write standard output.

This property controls the addition of the -filter switch, treat this property as a boolean.

property forwardinput

Sequence of a forward primer to check.

This controls the addition of the -forwardinput parameter and its associated value. Set this property to the argument value required.

property gcclamp

The required number of Gs and Cs at the 3’ of each primer.

This controls the addition of the -gcclamp parameter and its associated value. Set this property to the argument value required.

property help

Report command line options.

More information on associated and general qualifiers can be found with -help -verbose

This property controls the addition of the -help switch, treat this property as a boolean.

property hybridprobe

Find an internal oligo to use as a hyb probe.

This controls the addition of the -hybridprobe parameter and its associated value. Set this property to the argument value required.

property includedregion

Subregion of the sequence in which to pick primers.

This controls the addition of the -includedregion parameter and its associated value. Set this property to the argument value required.

property maxdifftm

Maximum difference in melting temperatures between forward and reverse primers.

This controls the addition of the -maxdifftm parameter and its associated value. Set this property to the argument value required.

property maxgc

Maximum GC% for a primer.

This controls the addition of the -maxgc parameter and its associated value. Set this property to the argument value required.

property maxmispriming

Maximum allowed similarity of primers to sequences in library specified by -mispriminglibrary

This controls the addition of the -maxmispriming parameter and its associated value. Set this property to the argument value required.

property maxpolyx

Maximum allowable mononucleotide repeat length in a primer.

This controls the addition of the -maxpolyx parameter and its associated value. Set this property to the argument value required.

property maxsize

Maximum length of a primer oligo.

This controls the addition of the -maxsize parameter and its associated value. Set this property to the argument value required.

property maxtm

Maximum melting temperature for a primer oligo.

This controls the addition of the -maxtm parameter and its associated value. Set this property to the argument value required.

property mingc

Minimum GC% for a primer.

This controls the addition of the -mingc parameter and its associated value. Set this property to the argument value required.

property minsize

Minimum length of a primer oligo.

This controls the addition of the -minsize parameter and its associated value. Set this property to the argument value required.

property mintm

Minimum melting temperature for a primer oligo.

This controls the addition of the -mintm parameter and its associated value. Set this property to the argument value required.

property mishyblibraryfile

Library file of seqs to avoid internal oligo hybridisation.

Option added in EMBOSS 6.1.0, replacing -oligomishyblibraryfile

This controls the addition of the -mishyblibraryfile parameter and its associated value. Set this property to the argument value required.

property mispriminglibraryfile

File containing library of sequences to avoid amplifying

This controls the addition of the -mispriminglibraryfile parameter and its associated value. Set this property to the argument value required.

property numreturn

Maximum number of primer pairs to return.

This controls the addition of the -numreturn parameter and its associated value. Set this property to the argument value required.

property oanyself

Maximum allowable alignment score for self-complementarity.”),

Option added in EMBOSS 6.1.0, replacing -oligoselfany

This controls the addition of the -oanyself parameter and its associated value. Set this property to the argument value required.

property odnaconc

Nanomolar concentration of internal oligo in the hybridisation.

Option added in EMBOSS 6.1.0, replacing -oligodnaconc

This controls the addition of the -odnaconc parameter and its associated value. Set this property to the argument value required.

property oendself

Max 3’-anchored self-complementarity global alignment score.

Option added in EMBOSS 6.1.0, replacing -oligoselfend

This controls the addition of the -oendself parameter and its associated value. Set this property to the argument value required.

property oexcludedregion

Do not pick internal oligos in this region.”),

Option added in EMBOSS 6.1.0, replacing -oligoexcludedregion.

This controls the addition of the -oexcludedregion parameter and its associated value. Set this property to the argument value required.

property ogcmax

Maximum GC% for internal oligo.”),

Option added in EMBOSS 6.1.0, replacing -oligomaxgc

This controls the addition of the -ogcmax parameter and its associated value. Set this property to the argument value required.

property ogcmin

Minimum GC% for internal oligo.

Option added in EMBOSS 6.1.0, replacing -oligomingc

This controls the addition of the -ogcmin parameter and its associated value. Set this property to the argument value required.

property ogcopt

Optimum GC% for internal oligo.”

Option added in EMBOSS 6.1.0, replacing -oligoogcpercent

This controls the addition of the -ogcopt parameter and its associated value. Set this property to the argument value required.

property ogcpercent

Optimum GC% for a primer.

This controls the addition of the -ogcpercent parameter and its associated value. Set this property to the argument value required.

property oligodnaconc

Nanomolar concentration of internal oligo in the hybridisation.

Option replaced in EMBOSS 6.1.0 by -odnaconc

This controls the addition of the -oligodnaconc parameter and its associated value. Set this property to the argument value required.

property oligoexcludedregion

Do not pick internal oligos in this region (OBSOLETE).”),

Option replaced in EMBOSS 6.1.0 by -oexcluderegion.

This controls the addition of the -oligoexcludedregion parameter and its associated value. Set this property to the argument value required.

property oligoinput

Sequence of the internal oligo.

This controls the addition of the -oligoinput parameter and its associated value. Set this property to the argument value required.

property oligomaxgc

Maximum GC% for internal oligo.

Option replaced in EMBOSS 6.1.0 by -ogcmax

This controls the addition of the -oligomaxgc parameter and its associated value. Set this property to the argument value required.

property oligomaxmishyb

Maximum alignment score for hybridisation of internal oligo to

library specified by -oligomishyblibraryfile (OBSOLETE).

Option replaced in EMBOSS 6.1.0 by -omishybmax

This controls the addition of the -oligomaxmishyb parameter and its associated value. Set this property to the argument value required.

property oligomaxpolyx

Maximum length of mononucleotide repeat in internal oligo (OBSOLETE).

Option replaced in EMBOSS 6.1.0 by -opolyxmax

This controls the addition of the -oligomaxpolyx parameter and its associated value. Set this property to the argument value required.

property oligomaxsize

Maximum length of internal oligo (OBSOLETE).

Option replaced in EMBOSS 6.1.0 by -omaxsize.

This controls the addition of the -oligomaxsize parameter and its associated value. Set this property to the argument value required.

property oligomaxtm

Maximum melting temperature of internal oligo (OBSOLETE).

Option replaced in EMBOSS 6.1.0 by -otmmax.

This controls the addition of the -oligomaxtm parameter and its associated value. Set this property to the argument value required.

property oligomingc

Minimum GC% for internal oligo (OBSOLETE).

Option replaced in EMBOSS 6.1.0 by -ogcmin.

This controls the addition of the -oligomingc parameter and its associated value. Set this property to the argument value required.

property oligominsize

Minimum length of internal oligo (OBSOLETE).”),

Option replaced in EMBOSS 6.1.0 by -ominsize.

This controls the addition of the -oligominsize parameter and its associated value. Set this property to the argument value required.

property oligomintm

Minimum melting temperature of internal oligo (OBSOLETE).

Option replaced in EMBOSS 6.1.0 by -otmmin.

This controls the addition of the -oligomintm parameter and its associated value. Set this property to the argument value required.

property oligomishyblibraryfile

Library file of seqs to avoid internal oligo hybridisation (OBSOLETE).

Option replaced in EMBOSS 6.1.0 by -mishyblibraryfile

This controls the addition of the -oligomishyblibraryfile parameter and its associated value. Set this property to the argument value required.

property oligoogcpercent

Optimum GC% for internal oligo (OBSOLETE).

Option replaced in EMBOSS 6.1.0 by -ogcopt.

This controls the addition of the -oligoogcpercent parameter and its associated value. Set this property to the argument value required.

property oligosaltconc

Millimolar concentration of salt in the hybridisation.”),

Option replaced in EMBOSS 6.1.0 by -osaltconc

This controls the addition of the -oligosaltconc parameter and its associated value. Set this property to the argument value required.

property oligoselfany

Maximum allowable alignment score for self-complementarity (OBSOLETE).

Option replaced in EMBOSS 6.1.0 by -oanyself

This controls the addition of the -oligoselfany parameter and its associated value. Set this property to the argument value required.

property oligoselfend

Maximum allowable 3’-anchored global alignment score “

for self-complementarity (OBSOLETE).

Option replaced in EMBOSS 6.1.0 by -oendself

This controls the addition of the -oligoselfend parameter and its associated value. Set this property to the argument value required.

property oligosize

Optimum length of internal oligo (OBSOLETE).

Option replaced in EMBOSS 6.1.0 by -osizeopt.

This controls the addition of the -oligosize parameter and its associated value. Set this property to the argument value required.

property oligotm

Optimum melting temperature of internal oligo (OBSOLETE).

Option replaced in EMBOSS 6.1.0 by -otmopt.

This controls the addition of the -oligotm parameter and its associated value. Set this property to the argument value required.

property omaxsize

Maximum length of internal oligo.

Option added in EMBOSS 6.1.0, replaces -oligomaxsize

This controls the addition of the -omaxsize parameter and its associated value. Set this property to the argument value required.

property ominsize

Minimum length of internal oligo.”

Option added in EMBOSS 6.1.0, replaces -oligominsize

This controls the addition of the -ominsize parameter and its associated value. Set this property to the argument value required.

property omishybmax

Maximum alignment score for hybridisation of internal oligo to

library specified by -mishyblibraryfile.

Option added in EMBOSS 6.1.0, replacing -oligomaxmishyb

This controls the addition of the -omishybmax parameter and its associated value. Set this property to the argument value required.

property opolyxmax

Maximum length of mononucleotide repeat in internal oligo.”),

Option added in EMBOSS 6.1.0, replacing -oligomaxpolyx

This controls the addition of the -opolyxmax parameter and its associated value. Set this property to the argument value required.

property options

Prompt for standard and additional values.

If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

This property controls the addition of the -options switch, treat this property as a boolean.

property opttm

Optimum melting temperature for a primer oligo.

Option added in EMBOSS 6.6.0, replacing -otm

This controls the addition of the -opttm parameter and its associated value. Set this property to the argument value required.

property osaltconc

Millimolar concentration of salt in the hybridisation.”),

Option added in EMBOSS 6.1.0, replacing -oligosaltconc

This controls the addition of the -osaltconc parameter and its associated value. Set this property to the argument value required.

property osize

Optimum length of a primer oligo.

This controls the addition of the -osize parameter and its associated value. Set this property to the argument value required.

property osizeopt

Optimum length of internal oligo.

Option added in EMBOSS 6.1.0, replaces -oligosize

This controls the addition of the -osizeopt parameter and its associated value. Set this property to the argument value required.

property otm

Melting temperature for primer oligo (OBSOLETE).

Option replaced in EMBOSS 6.6.0 by -opttm

This controls the addition of the -otm parameter and its associated value. Set this property to the argument value required.

property otmmax

Maximum melting temperature of internal oligo.

Option added in EMBOSS 6.1.0, replacing -oligomaxtm

This controls the addition of the -otmmax parameter and its associated value. Set this property to the argument value required.

property otmmin

Minimum melting temperature of internal oligo.

Option added in EMBOSS 6.1.0, replacing -oligomintm

This controls the addition of the -otmmin parameter and its associated value. Set this property to the argument value required.

property otmopt

Optimum melting temperature of internal oligo.

Option added in EMBOSS 6.1.0.

This controls the addition of the -otmopt parameter and its associated value. Set this property to the argument value required.

property outfile

Output filename

This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

property prange

Acceptable range of length for the PCR product.

Option added in EMBOSS 6.1.0, replacing -productsizerange

This controls the addition of the -prange parameter and its associated value. Set this property to the argument value required.

property productmaxtm

Maximum allowed melting temperature for the amplicon (OBSOLETE).

Option replaced in EMBOSS 6.1.0 by -ptmmax

This controls the addition of the -productmaxtm parameter and its associated value. Set this property to the argument value required.

property productmintm

Minimum allowed melting temperature for the amplicon (OBSOLETE)

Option replaced in EMBOSS 6.1.0 by -ptmmin

This controls the addition of the -productmintm parameter and its associated value. Set this property to the argument value required.

property productosize

Optimum size for the PCR product (OBSOLETE).

Option replaced in EMBOSS 6.1.0 by -psizeopt

This controls the addition of the -productosize parameter and its associated value. Set this property to the argument value required.

property productotm

Optimum melting temperature for the PCR product (OBSOLETE).

Option replaced in EMBOSS 6.1.0 by -ptmopt

This controls the addition of the -productotm parameter and its associated value. Set this property to the argument value required.

property productsizerange

Acceptable range of length for the PCR product (OBSOLETE).

Option replaced in EMBOSS 6.1.0 by -prange

This controls the addition of the -productsizerange parameter and its associated value. Set this property to the argument value required.

property psizeopt

Optimum size for the PCR product.

Option added in EMBOSS 6.1.0, replacing -productosize

This controls the addition of the -psizeopt parameter and its associated value. Set this property to the argument value required.

property ptmmax

Maximum allowed melting temperature for the amplicon.”),

Option added in EMBOSS 6.1.0, replacing -productmaxtm

This controls the addition of the -ptmmax parameter and its associated value. Set this property to the argument value required.

property ptmmin

Minimum allowed melting temperature for the amplicon.”),

Option added in EMBOSS 6.1.0, replacing -productmintm

This controls the addition of the -ptmmin parameter and its associated value. Set this property to the argument value required.

property ptmopt

Optimum melting temperature for the PCR product.

Option added in EMBOSS 6.1.0, replacing -productotm

This controls the addition of the -ptmopt parameter and its associated value. Set this property to the argument value required.

property reverseinput

Sequence of a reverse primer to check.

This controls the addition of the -reverseinput parameter and its associated value. Set this property to the argument value required.

property saltconc

Millimolar salt concentration in the PCR.

This controls the addition of the -saltconc parameter and its associated value. Set this property to the argument value required.

property sequence

Sequence to choose primers from.

This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.

property stdout

Write standard output.

This property controls the addition of the -stdout switch, treat this property as a boolean.

property target

Sequence to target for flanking primers.

This controls the addition of the -target parameter and its associated value. Set this property to the argument value required.

property task

Tell eprimer3 what task to perform.

This controls the addition of the -task parameter and its associated value. Set this property to the argument value required.

property verbose

Report some/full command line options

This property controls the addition of the -verbose switch, treat this property as a boolean.

property warning

Report warnings.

This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.PrimerSearchCommandline(cmd='primersearch', **kwargs)

Bases: Bio.Emboss.Applications._EmbossCommandLine

Commandline object for the primersearch program from EMBOSS.

__init__(self, cmd='primersearch', **kwargs)

Initialize the class.

property auto

Turn off prompts.

Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

This property controls the addition of the -auto switch, treat this property as a boolean.

property debug

Write debug output to program.dbg.

This property controls the addition of the -debug switch, treat this property as a boolean.

property die

Report dying program messages.

This property controls the addition of the -die switch, treat this property as a boolean.

property error

Report errors.

This property controls the addition of the -error switch, treat this property as a boolean.

property filter

Read standard input, write standard output.

This property controls the addition of the -filter switch, treat this property as a boolean.

property help

Report command line options.

More information on associated and general qualifiers can be found with -help -verbose

This property controls the addition of the -help switch, treat this property as a boolean.

property infile

File containing the primer pairs to search for.

This controls the addition of the -infile parameter and its associated value. Set this property to the argument value required.

property mismatchpercent

Allowed percentage mismatch (any integer value, default 0).

This controls the addition of the -mismatchpercent parameter and its associated value. Set this property to the argument value required.

property options

Prompt for standard and additional values.

If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

This property controls the addition of the -options switch, treat this property as a boolean.

property outfile

Output filename

This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

property seqall

Sequence to look for the primer pairs in.

This controls the addition of the -seqall parameter and its associated value. Set this property to the argument value required.

property snucleotide

Sequences are nucleotide (boolean)

This controls the addition of the -snucleotide parameter and its associated value. Set this property to the argument value required.

property sprotein

Sequences are protein (boolean)

This controls the addition of the -sprotein parameter and its associated value. Set this property to the argument value required.

property stdout

Write standard output.

This property controls the addition of the -stdout switch, treat this property as a boolean.

property verbose

Report some/full command line options

This property controls the addition of the -verbose switch, treat this property as a boolean.

property warning

Report warnings.

This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.FDNADistCommandline(cmd='fdnadist', **kwargs)

Bases: Bio.Emboss.Applications._EmbossCommandLine

Commandline object for the fdnadist program from EMBOSS.

fdnadist is an EMBOSS wrapper for the PHYLIP program dnadist for calulating distance matrices from DNA sequence files.

__init__(self, cmd='fdnadist', **kwargs)

Initialize the class.

property auto

Turn off prompts.

Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

This property controls the addition of the -auto switch, treat this property as a boolean.

property basefreq

specify basefreqs

This controls the addition of the -basefreq parameter and its associated value. Set this property to the argument value required.

property categories

File of substitution rate categories

This controls the addition of the -categories parameter and its associated value. Set this property to the argument value required.

property debug

Write debug output to program.dbg.

This property controls the addition of the -debug switch, treat this property as a boolean.

property die

Report dying program messages.

This property controls the addition of the -die switch, treat this property as a boolean.

property error

Report errors.

This property controls the addition of the -error switch, treat this property as a boolean.

property filter

Read standard input, write standard output.

This property controls the addition of the -filter switch, treat this property as a boolean.

property freqsfrom

use emprical base freqs

This controls the addition of the -freqsfrom parameter and its associated value. Set this property to the argument value required.

property gamma

gamma [g, i,n]

This controls the addition of the -gamma parameter and its associated value. Set this property to the argument value required.

property gammacoefficient

value for gamma (> 0.001)

This controls the addition of the -gammacoefficient parameter and its associated value. Set this property to the argument value required.

property help

Report command line options.

More information on associated and general qualifiers can be found with -help -verbose

This property controls the addition of the -help switch, treat this property as a boolean.

property invarfrac

proportoin of invariant sites

This controls the addition of the -invarfrac parameter and its associated value. Set this property to the argument value required.

property lower

lower triangle matrix (y/N)

This controls the addition of the -lower parameter and its associated value. Set this property to the argument value required.

property method

sub. model [f,k,j,l,s]

This controls the addition of the -method parameter and its associated value. Set this property to the argument value required.

property ncategories

number of rate catergories (1-9)

This controls the addition of the -ncategories parameter and its associated value. Set this property to the argument value required.

property options

Prompt for standard and additional values.

If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

This property controls the addition of the -options switch, treat this property as a boolean.

property outfile

Output filename

This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

property rate

rate for each category

This controls the addition of the -rate parameter and its associated value. Set this property to the argument value required.

property sequence

seq file to use (phylip)

This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.

property stdout

Write standard output.

This property controls the addition of the -stdout switch, treat this property as a boolean.

property ttratio

ts/tv ratio

This controls the addition of the -ttratio parameter and its associated value. Set this property to the argument value required.

property verbose

Report some/full command line options

This property controls the addition of the -verbose switch, treat this property as a boolean.

property warning

Report warnings.

This property controls the addition of the -warning switch, treat this property as a boolean.

property weights

weights file

This controls the addition of the -weights parameter and its associated value. Set this property to the argument value required.

class Bio.Emboss.Applications.FTreeDistCommandline(cmd='ftreedist', **kwargs)

Bases: Bio.Emboss.Applications._EmbossCommandLine

Commandline object for the ftreedist program from EMBOSS.

ftreedist is an EMBOSS wrapper for the PHYLIP program treedist used for calulating distance measures between phylogentic trees.

__init__(self, cmd='ftreedist', **kwargs)

Initialize the class.

property auto

Turn off prompts.

Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

This property controls the addition of the -auto switch, treat this property as a boolean.

property debug

Write debug output to program.dbg.

This property controls the addition of the -debug switch, treat this property as a boolean.

property die

Report dying program messages.

This property controls the addition of the -die switch, treat this property as a boolean.

property dtype

distance type ([S]ymetric, [b]ranch score)

This controls the addition of the -dtype parameter and its associated value. Set this property to the argument value required.

property error

Report errors.

This property controls the addition of the -error switch, treat this property as a boolean.

property filter

Read standard input, write standard output.

This property controls the addition of the -filter switch, treat this property as a boolean.

property help

Report command line options.

More information on associated and general qualifiers can be found with -help -verbose

This property controls the addition of the -help switch, treat this property as a boolean.

property intreefile

tree file to score (phylip)

This controls the addition of the -intreefile parameter and its associated value. Set this property to the argument value required.

property noroot

treat trees as rooted [N/y]

This controls the addition of the -noroot parameter and its associated value. Set this property to the argument value required.

property options

Prompt for standard and additional values.

If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

This property controls the addition of the -options switch, treat this property as a boolean.

property outfile

Output filename

This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

property outgrno

which taxon to root the trees with (starts from 0)

This controls the addition of the -outgrno parameter and its associated value. Set this property to the argument value required.

property pairing

tree pairing method ([A]djacent pairs, all [p]ossible pairs)

This controls the addition of the -pairing parameter and its associated value. Set this property to the argument value required.

property stdout

Write standard output.

This property controls the addition of the -stdout switch, treat this property as a boolean.

property style

output style - [V]erbose, [f]ill, [s]parse

This controls the addition of the -style parameter and its associated value. Set this property to the argument value required.

property verbose

Report some/full command line options

This property controls the addition of the -verbose switch, treat this property as a boolean.

property warning

Report warnings.

This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.FNeighborCommandline(cmd='fneighbor', **kwargs)

Bases: Bio.Emboss.Applications._EmbossCommandLine

Commandline object for the fneighbor program from EMBOSS.

fneighbor is an EMBOSS wrapper for the PHYLIP program neighbor used for calulating neighbor-joining or UPGMA trees from distance matrices.

__init__(self, cmd='fneighbor', **kwargs)

Initialize the class.

property auto

Turn off prompts.

Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

This property controls the addition of the -auto switch, treat this property as a boolean.

property datafile

dist file to use (phylip)

This controls the addition of the -datafile parameter and its associated value. Set this property to the argument value required.

property debug

Write debug output to program.dbg.

This property controls the addition of the -debug switch, treat this property as a boolean.

property die

Report dying program messages.

This property controls the addition of the -die switch, treat this property as a boolean.

property error

Report errors.

This property controls the addition of the -error switch, treat this property as a boolean.

property filter

Read standard input, write standard output.

This property controls the addition of the -filter switch, treat this property as a boolean.

property help

Report command line options.

More information on associated and general qualifiers can be found with -help -verbose

This property controls the addition of the -help switch, treat this property as a boolean.

property jumble

randommise input order (Y/n)

This controls the addition of the -jumble parameter and its associated value. Set this property to the argument value required.

property matrixtype

is martrix [S]quare pr [u]pper or [l]ower

This controls the addition of the -matrixtype parameter and its associated value. Set this property to the argument value required.

property options

Prompt for standard and additional values.

If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

This property controls the addition of the -options switch, treat this property as a boolean.

property outfile

Output filename

This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

property outgrno

taxon to use as OG

This controls the addition of the -outgrno parameter and its associated value. Set this property to the argument value required.

property outtreefile

filename for output tree

This controls the addition of the -outtreefile parameter and its associated value. Set this property to the argument value required.

property progress

print progress (Y/n)

This controls the addition of the -progress parameter and its associated value. Set this property to the argument value required.

property seed

provide a random seed

This controls the addition of the -seed parameter and its associated value. Set this property to the argument value required.

property stdout

Write standard output.

This property controls the addition of the -stdout switch, treat this property as a boolean.

property treeprint

print tree (Y/n)

This controls the addition of the -treeprint parameter and its associated value. Set this property to the argument value required.

property treetype

nj or UPGMA tree (n/u)

This controls the addition of the -treetype parameter and its associated value. Set this property to the argument value required.

property trout

write tree (Y/n)

This controls the addition of the -trout parameter and its associated value. Set this property to the argument value required.

property verbose

Report some/full command line options

This property controls the addition of the -verbose switch, treat this property as a boolean.

property warning

Report warnings.

This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.FSeqBootCommandline(cmd='fseqboot', **kwargs)

Bases: Bio.Emboss.Applications._EmbossCommandLine

Commandline object for the fseqboot program from EMBOSS.

fseqboot is an EMBOSS wrapper for the PHYLIP program seqboot used to pseudo-sample alignment files.

__init__(self, cmd='fseqboot', **kwargs)

Initialize the class.

property auto

Turn off prompts.

Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

This property controls the addition of the -auto switch, treat this property as a boolean.

property blocksize

print progress (Y/n)

This controls the addition of the -blocksize parameter and its associated value. Set this property to the argument value required.

property catergories

file of input categories

This controls the addition of the -categories parameter and its associated value. Set this property to the argument value required.

property debug

Write debug output to program.dbg.

This property controls the addition of the -debug switch, treat this property as a boolean.

property die

Report dying program messages.

This property controls the addition of the -die switch, treat this property as a boolean.

property dotdiff

Use dot-differencing? [Y/n]

This controls the addition of the -dotdiff parameter and its associated value. Set this property to the argument value required.

property error

Report errors.

This property controls the addition of the -error switch, treat this property as a boolean.

property filter

Read standard input, write standard output.

This property controls the addition of the -filter switch, treat this property as a boolean.

property fracsample

fraction to resample

This controls the addition of the -fracsample parameter and its associated value. Set this property to the argument value required.

property help

Report command line options.

More information on associated and general qualifiers can be found with -help -verbose

This property controls the addition of the -help switch, treat this property as a boolean.

property jusweights

what to write out [D]atasets of just [w]eights

This controls the addition of the -justweights parameter and its associated value. Set this property to the argument value required.

property options

Prompt for standard and additional values.

If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

This property controls the addition of the -options switch, treat this property as a boolean.

property outfile

Output filename

This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

property regular

absolute number to resample

This controls the addition of the -regular parameter and its associated value. Set this property to the argument value required.

property reps

how many replicates, defaults to 100)

This controls the addition of the -reps parameter and its associated value. Set this property to the argument value required.

property rewriteformat

output format ([P]hyilp, [n]exus, [x]ml

This controls the addition of the -rewriteformat parameter and its associated value. Set this property to the argument value required.

property seed

specify random seed

This controls the addition of the -seed parameter and its associated value. Set this property to the argument value required.

property seqtype

output format ([D]na, [p]rotein, [r]na

This controls the addition of the -seqtype parameter and its associated value. Set this property to the argument value required.

property sequence

seq file to sample (phylip)

This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.

property stdout

Write standard output.

This property controls the addition of the -stdout switch, treat this property as a boolean.

property test

specify operation, default is bootstrap

This controls the addition of the -test parameter and its associated value. Set this property to the argument value required.

property verbose

Report some/full command line options

This property controls the addition of the -verbose switch, treat this property as a boolean.

property warning

Report warnings.

This property controls the addition of the -warning switch, treat this property as a boolean.

property weights

weights file

This controls the addition of the -weights parameter and its associated value. Set this property to the argument value required.

class Bio.Emboss.Applications.FDNAParsCommandline(cmd='fdnapars', **kwargs)

Bases: Bio.Emboss.Applications._EmbossCommandLine

Commandline object for the fdnapars program from EMBOSS.

fdnapars is an EMBOSS version of the PHYLIP program dnapars, for estimating trees from DNA sequences using parsiomny. Calling this command without providing a value for the option “-intreefile” will invoke “interactive mode” (and as a result fail if called with subprocess) if “-auto” is not set to true.

__init__(self, cmd='fdnapars', **kwargs)

Initialize the class.

property auto

Turn off prompts.

Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

This property controls the addition of the -auto switch, treat this property as a boolean.

property debug

Write debug output to program.dbg.

This property controls the addition of the -debug switch, treat this property as a boolean.

property die

Report dying program messages.

This property controls the addition of the -die switch, treat this property as a boolean.

property dotdiff

Use dot-differencing? [Y/n]

This controls the addition of the -dotdiff parameter and its associated value. Set this property to the argument value required.

property error

Report errors.

This property controls the addition of the -error switch, treat this property as a boolean.

property filter

Read standard input, write standard output.

This property controls the addition of the -filter switch, treat this property as a boolean.

property help

Report command line options.

More information on associated and general qualifiers can be found with -help -verbose

This property controls the addition of the -help switch, treat this property as a boolean.

property intreefile

Phylip tree file

This controls the addition of the -intreefile parameter and its associated value. Set this property to the argument value required.

property maxtrees

max trees to save during run

This controls the addition of the -maxtrees parameter and its associated value. Set this property to the argument value required.

property njumble

number of times to randomise input order (default is 0)

This controls the addition of the -njumble parameter and its associated value. Set this property to the argument value required.

property options

Prompt for standard and additional values.

If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

This property controls the addition of the -options switch, treat this property as a boolean.

property outfile

Output filename

This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

property outgrno

Specify outgroup

This controls the addition of the -outgrno parameter and its associated value. Set this property to the argument value required.

property outtreefile

filename for output tree

This controls the addition of the -outtreefile parameter and its associated value. Set this property to the argument value required.

property rearrange

Rearrange on just 1 best tree (Y/n)

This controls the addition of the -rearrange parameter and its associated value. Set this property to the argument value required.

property seed

provide random seed

This controls the addition of the -seed parameter and its associated value. Set this property to the argument value required.

property sequence

seq file to use (phylip)

This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.

property stdout

Write standard output.

This property controls the addition of the -stdout switch, treat this property as a boolean.

property thorough

more thorough search (Y/n)

This controls the addition of the -thorough parameter and its associated value. Set this property to the argument value required.

property thresh

Use threshold parsimony (y/N)

This controls the addition of the -thresh parameter and its associated value. Set this property to the argument value required.

property threshold

Threshold value

This controls the addition of the -threshold parameter and its associated value. Set this property to the argument value required.

property transversion

Use tranversion parsimony (y/N)

This controls the addition of the -transversion parameter and its associated value. Set this property to the argument value required.

property trout

Write trees to file (Y/n)

This controls the addition of the -trout parameter and its associated value. Set this property to the argument value required.

property verbose

Report some/full command line options

This property controls the addition of the -verbose switch, treat this property as a boolean.

property warning

Report warnings.

This property controls the addition of the -warning switch, treat this property as a boolean.

property weights

weights file

This controls the addition of the -weights parameter and its associated value. Set this property to the argument value required.

class Bio.Emboss.Applications.FProtParsCommandline(cmd='fprotpars', **kwargs)

Bases: Bio.Emboss.Applications._EmbossCommandLine

Commandline object for the fdnapars program from EMBOSS.

fprotpars is an EMBOSS version of the PHYLIP program protpars, for estimating trees from protein sequences using parsiomny. Calling this command without providing a value for the option “-intreefile” will invoke “interactive mode” (and as a result fail if called with subprocess) if “-auto” is not set to true.

__init__(self, cmd='fprotpars', **kwargs)

Initialize the class.

property auto

Turn off prompts.

Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

This property controls the addition of the -auto switch, treat this property as a boolean.

property debug

Write debug output to program.dbg.

This property controls the addition of the -debug switch, treat this property as a boolean.

property die

Report dying program messages.

This property controls the addition of the -die switch, treat this property as a boolean.

property dotdiff

Use dot-differencing? [Y/n]

This controls the addition of the -dotdiff parameter and its associated value. Set this property to the argument value required.

property error

Report errors.

This property controls the addition of the -error switch, treat this property as a boolean.

property filter

Read standard input, write standard output.

This property controls the addition of the -filter switch, treat this property as a boolean.

property help

Report command line options.

More information on associated and general qualifiers can be found with -help -verbose

This property controls the addition of the -help switch, treat this property as a boolean.

property intreefile

Phylip tree file to score

This controls the addition of the -intreefile parameter and its associated value. Set this property to the argument value required.

property njumble

number of times to randomise input order (default is 0)

This controls the addition of the -njumble parameter and its associated value. Set this property to the argument value required.

property options

Prompt for standard and additional values.

If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

This property controls the addition of the -options switch, treat this property as a boolean.

property outfile

Output filename

This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

property outgrno

Specify outgroup

This controls the addition of the -outgrno parameter and its associated value. Set this property to the argument value required.

property outtreefile

phylip tree output file

This controls the addition of the -outtreefile parameter and its associated value. Set this property to the argument value required.

property seed

provide random seed

This controls the addition of the -seed parameter and its associated value. Set this property to the argument value required.

property sequence

seq file to use (phylip)

This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.

property stdout

Write standard output.

This property controls the addition of the -stdout switch, treat this property as a boolean.

property thresh

Use threshold parsimony (y/N)

This controls the addition of the -thresh parameter and its associated value. Set this property to the argument value required.

property threshold

Threshold value

This controls the addition of the -threshold parameter and its associated value. Set this property to the argument value required.

property trout

Write trees to file (Y/n)

This controls the addition of the -trout parameter and its associated value. Set this property to the argument value required.

property verbose

Report some/full command line options

This property controls the addition of the -verbose switch, treat this property as a boolean.

property warning

Report warnings.

This property controls the addition of the -warning switch, treat this property as a boolean.

property weights

weights file

This controls the addition of the -weights parameter and its associated value. Set this property to the argument value required.

property whichcode

which genetic code, [U,M,V,F,Y]]

This controls the addition of the -whichcode parameter and its associated value. Set this property to the argument value required.

class Bio.Emboss.Applications.FProtDistCommandline(cmd='fprotdist', **kwargs)

Bases: Bio.Emboss.Applications._EmbossCommandLine

Commandline object for the fprotdist program from EMBOSS.

fprotdist is an EMBOSS wrapper for the PHYLIP program protdist used to estimate trees from protein sequences using parsimony

__init__(self, cmd='fprotdist', **kwargs)

Initialize the class.

property aacateg

Choose the category to use [G,C,H]

This controls the addition of the -aacateg parameter and its associated value. Set this property to the argument value required.

property auto

Turn off prompts.

Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

This property controls the addition of the -auto switch, treat this property as a boolean.

property basefreq

DNA base frequencies (space separated list)

This controls the addition of the -basefreq parameter and its associated value. Set this property to the argument value required.

property catergories

file of rates

This controls the addition of the -catergories parameter and its associated value. Set this property to the argument value required.

property debug

Write debug output to program.dbg.

This property controls the addition of the -debug switch, treat this property as a boolean.

property die

Report dying program messages.

This property controls the addition of the -die switch, treat this property as a boolean.

property ease

Pob change catergory (float between -0 and 1)

This controls the addition of the -ease parameter and its associated value. Set this property to the argument value required.

property error

Report errors.

This property controls the addition of the -error switch, treat this property as a boolean.

property filter

Read standard input, write standard output.

This property controls the addition of the -filter switch, treat this property as a boolean.

property gamma

gamma [g, i,c]

This controls the addition of the -gamma parameter and its associated value. Set this property to the argument value required.

property gammacoefficient

value for gamma (> 0.001)

This controls the addition of the -gammacoefficient parameter and its associated value. Set this property to the argument value required.

property help

Report command line options.

More information on associated and general qualifiers can be found with -help -verbose

This property controls the addition of the -help switch, treat this property as a boolean.

property invarcoefficient

float for variation of substitution rate among sites

This controls the addition of the -invarcoefficient parameter and its associated value. Set this property to the argument value required.

property method

sub. model [j,h,d,k,s,c]

This controls the addition of the -method parameter and its associated value. Set this property to the argument value required.

property ncategories

number of rate catergories (1-9)

This controls the addition of the -ncategories parameter and its associated value. Set this property to the argument value required.

property options

Prompt for standard and additional values.

If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

This property controls the addition of the -options switch, treat this property as a boolean.

property outfile

Output filename

This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

property rate

rate for each category

This controls the addition of the -rate parameter and its associated value. Set this property to the argument value required.

property sequence

seq file to use (phylip)

This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.

property stdout

Write standard output.

This property controls the addition of the -stdout switch, treat this property as a boolean.

property ttratio

Transition/transversion ratio (0-1)

This controls the addition of the -ttratio parameter and its associated value. Set this property to the argument value required.

property verbose

Report some/full command line options

This property controls the addition of the -verbose switch, treat this property as a boolean.

property warning

Report warnings.

This property controls the addition of the -warning switch, treat this property as a boolean.

property weights

weights file

This controls the addition of the -weights parameter and its associated value. Set this property to the argument value required.

property whichcode

genetic code [c,m,v,f,y]

This controls the addition of the -whichcode parameter and its associated value. Set this property to the argument value required.

class Bio.Emboss.Applications.FConsenseCommandline(cmd='fconsense', **kwargs)

Bases: Bio.Emboss.Applications._EmbossCommandLine

Commandline object for the fconsense program from EMBOSS.

fconsense is an EMBOSS wrapper for the PHYLIP program consense used to calculate consensus trees.

__init__(self, cmd='fconsense', **kwargs)

Initialize the class.

property auto

Turn off prompts.

Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

This property controls the addition of the -auto switch, treat this property as a boolean.

property debug

Write debug output to program.dbg.

This property controls the addition of the -debug switch, treat this property as a boolean.

property die

Report dying program messages.

This property controls the addition of the -die switch, treat this property as a boolean.

property error

Report errors.

This property controls the addition of the -error switch, treat this property as a boolean.

property filter

Read standard input, write standard output.

This property controls the addition of the -filter switch, treat this property as a boolean.

property help

Report command line options.

More information on associated and general qualifiers can be found with -help -verbose

This property controls the addition of the -help switch, treat this property as a boolean.

property intreefile

file with phylip trees to make consensus from

This controls the addition of the -intreefile parameter and its associated value. Set this property to the argument value required.

property method

consensus method [s, mr, MRE, ml]

This controls the addition of the -method parameter and its associated value. Set this property to the argument value required.

property mlfrac

cut-off freq for branch to appear in consensus (0.5-1.0)

This controls the addition of the -mlfrac parameter and its associated value. Set this property to the argument value required.

property options

Prompt for standard and additional values.

If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

This property controls the addition of the -options switch, treat this property as a boolean.

property outfile

Output filename

This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

property outgrno

OTU to use as outgroup (starts from 0)

This controls the addition of the -outgrno parameter and its associated value. Set this property to the argument value required.

property outtreefile

Phylip tree output file (optional)

This controls the addition of the -outtreefile parameter and its associated value. Set this property to the argument value required.

property root

treat trees as rooted (YES, no)

This controls the addition of the -root parameter and its associated value. Set this property to the argument value required.

property stdout

Write standard output.

This property controls the addition of the -stdout switch, treat this property as a boolean.

property trout

treat trees as rooted (YES, no)

This controls the addition of the -trout parameter and its associated value. Set this property to the argument value required.

property verbose

Report some/full command line options

This property controls the addition of the -verbose switch, treat this property as a boolean.

property warning

Report warnings.

This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.WaterCommandline(cmd='water', **kwargs)

Bases: Bio.Emboss.Applications._EmbossCommandLine

Commandline object for the water program from EMBOSS.

__init__(self, cmd='water', **kwargs)

Initialize the class.

property aformat

Display output in a different specified output format

This controls the addition of the -aformat parameter and its associated value. Set this property to the argument value required.

property asequence

First sequence to align

This controls the addition of the -asequence parameter and its associated value. Set this property to the argument value required.

property auto

Turn off prompts.

Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

This property controls the addition of the -auto switch, treat this property as a boolean.

property brief

Display brief identity and similarity

This property controls the addition of the -brief switch, treat this property as a boolean.

property bsequence

Second sequence to align

This controls the addition of the -bsequence parameter and its associated value. Set this property to the argument value required.

property datafile

Matrix file

This controls the addition of the -datafile parameter and its associated value. Set this property to the argument value required.

property debug

Write debug output to program.dbg.

This property controls the addition of the -debug switch, treat this property as a boolean.

property die

Report dying program messages.

This property controls the addition of the -die switch, treat this property as a boolean.

property error

Report errors.

This property controls the addition of the -error switch, treat this property as a boolean.

property filter

Read standard input, write standard output.

This property controls the addition of the -filter switch, treat this property as a boolean.

property gapextend

Gap extension penalty

This controls the addition of the -gapextend parameter and its associated value. Set this property to the argument value required.

property gapopen

Gap open penalty

This controls the addition of the -gapopen parameter and its associated value. Set this property to the argument value required.

property help

Report command line options.

More information on associated and general qualifiers can be found with -help -verbose

This property controls the addition of the -help switch, treat this property as a boolean.

property nobrief

Display extended identity and similarity

This property controls the addition of the -nobrief switch, treat this property as a boolean.

property options

Prompt for standard and additional values.

If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

This property controls the addition of the -options switch, treat this property as a boolean.

property outfile

Output filename

This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

property similarity

Display percent identity and similarity

This controls the addition of the -similarity parameter and its associated value. Set this property to the argument value required.

property snucleotide

Sequences are nucleotide (boolean)

This controls the addition of the -snucleotide parameter and its associated value. Set this property to the argument value required.

property sprotein

Sequences are protein (boolean)

This controls the addition of the -sprotein parameter and its associated value. Set this property to the argument value required.

property stdout

Write standard output.

This property controls the addition of the -stdout switch, treat this property as a boolean.

property verbose

Report some/full command line options

This property controls the addition of the -verbose switch, treat this property as a boolean.

property warning

Report warnings.

This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.NeedleCommandline(cmd='needle', **kwargs)

Bases: Bio.Emboss.Applications._EmbossCommandLine

Commandline object for the needle program from EMBOSS.

__init__(self, cmd='needle', **kwargs)

Initialize the class.

property aformat

Display output in a different specified output format

This controls the addition of the -aformat parameter and its associated value. Set this property to the argument value required.

property asequence

First sequence to align

This controls the addition of the -asequence parameter and its associated value. Set this property to the argument value required.

property auto

Turn off prompts.

Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

This property controls the addition of the -auto switch, treat this property as a boolean.

property brief

Display brief identity and similarity

This property controls the addition of the -brief switch, treat this property as a boolean.

property bsequence

Second sequence to align

This controls the addition of the -bsequence parameter and its associated value. Set this property to the argument value required.

property datafile

Matrix file

This controls the addition of the -datafile parameter and its associated value. Set this property to the argument value required.

property debug

Write debug output to program.dbg.

This property controls the addition of the -debug switch, treat this property as a boolean.

property die

Report dying program messages.

This property controls the addition of the -die switch, treat this property as a boolean.

property endextend

The score added to the end gap penality for each base or residue in the end gap.

This controls the addition of the -endextend parameter and its associated value. Set this property to the argument value required.

property endopen

The score taken away when an end gap is created.

This controls the addition of the -endopen parameter and its associated value. Set this property to the argument value required.

property endweight

Apply And gap penalties

This controls the addition of the -endweight parameter and its associated value. Set this property to the argument value required.

property error

Report errors.

This property controls the addition of the -error switch, treat this property as a boolean.

property filter

Read standard input, write standard output.

This property controls the addition of the -filter switch, treat this property as a boolean.

property gapextend

Gap extension penalty

This controls the addition of the -gapextend parameter and its associated value. Set this property to the argument value required.

property gapopen

Gap open penalty

This controls the addition of the -gapopen parameter and its associated value. Set this property to the argument value required.

property help

Report command line options.

More information on associated and general qualifiers can be found with -help -verbose

This property controls the addition of the -help switch, treat this property as a boolean.

property nobrief

Display extended identity and similarity

This property controls the addition of the -nobrief switch, treat this property as a boolean.

property options

Prompt for standard and additional values.

If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

This property controls the addition of the -options switch, treat this property as a boolean.

property outfile

Output filename

This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

property similarity

Display percent identity and similarity

This controls the addition of the -similarity parameter and its associated value. Set this property to the argument value required.

property snucleotide

Sequences are nucleotide (boolean)

This controls the addition of the -snucleotide parameter and its associated value. Set this property to the argument value required.

property sprotein

Sequences are protein (boolean)

This controls the addition of the -sprotein parameter and its associated value. Set this property to the argument value required.

property stdout

Write standard output.

This property controls the addition of the -stdout switch, treat this property as a boolean.

property verbose

Report some/full command line options

This property controls the addition of the -verbose switch, treat this property as a boolean.

property warning

Report warnings.

This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.NeedleallCommandline(cmd='needleall', **kwargs)

Bases: Bio.Emboss.Applications._EmbossCommandLine

Commandline object for the needleall program from EMBOSS.

__init__(self, cmd='needleall', **kwargs)

Initialize the class.

property aformat

Display output in a different specified output format

This controls the addition of the -aformat parameter and its associated value. Set this property to the argument value required.

property asequence

First sequence to align

This controls the addition of the -asequence parameter and its associated value. Set this property to the argument value required.

property auto

Turn off prompts.

Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

This property controls the addition of the -auto switch, treat this property as a boolean.

property brief

Display brief identity and similarity

This property controls the addition of the -brief switch, treat this property as a boolean.

property bsequence

Second sequence to align

This controls the addition of the -bsequence parameter and its associated value. Set this property to the argument value required.

property datafile

Matrix file

This controls the addition of the -datafile parameter and its associated value. Set this property to the argument value required.

property debug

Write debug output to program.dbg.

This property controls the addition of the -debug switch, treat this property as a boolean.

property die

Report dying program messages.

This property controls the addition of the -die switch, treat this property as a boolean.

property endextend

The score added to the end gap penality for each base or residue in the end gap.

This controls the addition of the -endextend parameter and its associated value. Set this property to the argument value required.

property endopen

The score taken away when an end gap is created.

This controls the addition of the -endopen parameter and its associated value. Set this property to the argument value required.

property endweight

Apply And gap penalties

This controls the addition of the -endweight parameter and its associated value. Set this property to the argument value required.

property error

Report errors.

This property controls the addition of the -error switch, treat this property as a boolean.

property errorfile

Error file to be written to.

This controls the addition of the -errorfile parameter and its associated value. Set this property to the argument value required.

property filter

Read standard input, write standard output.

This property controls the addition of the -filter switch, treat this property as a boolean.

property gapextend

Gap extension penalty

This controls the addition of the -gapextend parameter and its associated value. Set this property to the argument value required.

property gapopen

Gap open penalty

This controls the addition of the -gapopen parameter and its associated value. Set this property to the argument value required.

property help

Report command line options.

More information on associated and general qualifiers can be found with -help -verbose

This property controls the addition of the -help switch, treat this property as a boolean.

property minscore

Exclude alignments with scores below this threshold score.

This controls the addition of the -minscore parameter and its associated value. Set this property to the argument value required.

property nobrief

Display extended identity and similarity

This property controls the addition of the -nobrief switch, treat this property as a boolean.

property options

Prompt for standard and additional values.

If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

This property controls the addition of the -options switch, treat this property as a boolean.

property outfile

Output filename

This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

property similarity

Display percent identity and similarity

This controls the addition of the -similarity parameter and its associated value. Set this property to the argument value required.

property snucleotide

Sequences are nucleotide (boolean)

This controls the addition of the -snucleotide parameter and its associated value. Set this property to the argument value required.

property sprotein

Sequences are protein (boolean)

This controls the addition of the -sprotein parameter and its associated value. Set this property to the argument value required.

property stdout

Write standard output.

This property controls the addition of the -stdout switch, treat this property as a boolean.

property verbose

Report some/full command line options

This property controls the addition of the -verbose switch, treat this property as a boolean.

property warning

Report warnings.

This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.StretcherCommandline(cmd='stretcher', **kwargs)

Bases: Bio.Emboss.Applications._EmbossCommandLine

Commandline object for the stretcher program from EMBOSS.

__init__(self, cmd='stretcher', **kwargs)

Initialize the class.

property aformat

Display output in a different specified output format

This controls the addition of the -aformat parameter and its associated value. Set this property to the argument value required.

property asequence

First sequence to align

This controls the addition of the -asequence parameter and its associated value. Set this property to the argument value required.

property auto

Turn off prompts.

Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

This property controls the addition of the -auto switch, treat this property as a boolean.

property bsequence

Second sequence to align

This controls the addition of the -bsequence parameter and its associated value. Set this property to the argument value required.

property datafile

Matrix file

This controls the addition of the -datafile parameter and its associated value. Set this property to the argument value required.

property debug

Write debug output to program.dbg.

This property controls the addition of the -debug switch, treat this property as a boolean.

property die

Report dying program messages.

This property controls the addition of the -die switch, treat this property as a boolean.

property error

Report errors.

This property controls the addition of the -error switch, treat this property as a boolean.

property filter

Read standard input, write standard output.

This property controls the addition of the -filter switch, treat this property as a boolean.

property gapextend

Gap extension penalty

This controls the addition of the -gapextend parameter and its associated value. Set this property to the argument value required.

property gapopen

Gap open penalty

This controls the addition of the -gapopen parameter and its associated value. Set this property to the argument value required.

property help

Report command line options.

More information on associated and general qualifiers can be found with -help -verbose

This property controls the addition of the -help switch, treat this property as a boolean.

property options

Prompt for standard and additional values.

If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

This property controls the addition of the -options switch, treat this property as a boolean.

property outfile

Output filename

This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

property snucleotide

Sequences are nucleotide (boolean)

This controls the addition of the -snucleotide parameter and its associated value. Set this property to the argument value required.

property sprotein

Sequences are protein (boolean)

This controls the addition of the -sprotein parameter and its associated value. Set this property to the argument value required.

property stdout

Write standard output.

This property controls the addition of the -stdout switch, treat this property as a boolean.

property verbose

Report some/full command line options

This property controls the addition of the -verbose switch, treat this property as a boolean.

property warning

Report warnings.

This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.FuzznucCommandline(cmd='fuzznuc', **kwargs)

Bases: Bio.Emboss.Applications._EmbossCommandLine

Commandline object for the fuzznuc program from EMBOSS.

__init__(self, cmd='fuzznuc', **kwargs)

Initialize the class.

property auto

Turn off prompts.

Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

This property controls the addition of the -auto switch, treat this property as a boolean.

property complement

Search complementary strand

This controls the addition of the -complement parameter and its associated value. Set this property to the argument value required.

property debug

Write debug output to program.dbg.

This property controls the addition of the -debug switch, treat this property as a boolean.

property die

Report dying program messages.

This property controls the addition of the -die switch, treat this property as a boolean.

property error

Report errors.

This property controls the addition of the -error switch, treat this property as a boolean.

property filter

Read standard input, write standard output.

This property controls the addition of the -filter switch, treat this property as a boolean.

property help

Report command line options.

More information on associated and general qualifiers can be found with -help -verbose

This property controls the addition of the -help switch, treat this property as a boolean.

property options

Prompt for standard and additional values.

If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

This property controls the addition of the -options switch, treat this property as a boolean.

property outfile

Output filename

This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

property pattern

Search pattern, using standard IUPAC one-letter codes

This controls the addition of the -pattern parameter and its associated value. Set this property to the argument value required.

property pmismatch

Number of mismatches

This controls the addition of the -pmismatch parameter and its associated value. Set this property to the argument value required.

property rformat

Specify the report format to output in.

This controls the addition of the -rformat parameter and its associated value. Set this property to the argument value required.

property sequence

Sequence database USA

This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.

property stdout

Write standard output.

This property controls the addition of the -stdout switch, treat this property as a boolean.

property verbose

Report some/full command line options

This property controls the addition of the -verbose switch, treat this property as a boolean.

property warning

Report warnings.

This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.FuzzproCommandline(cmd='fuzzpro', **kwargs)

Bases: Bio.Emboss.Applications._EmbossCommandLine

Commandline object for the fuzzpro program from EMBOSS.

__init__(self, cmd='fuzzpro', **kwargs)

Initialize the class.

property auto

Turn off prompts.

Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

This property controls the addition of the -auto switch, treat this property as a boolean.

property debug

Write debug output to program.dbg.

This property controls the addition of the -debug switch, treat this property as a boolean.

property die

Report dying program messages.

This property controls the addition of the -die switch, treat this property as a boolean.

property error

Report errors.

This property controls the addition of the -error switch, treat this property as a boolean.

property filter

Read standard input, write standard output.

This property controls the addition of the -filter switch, treat this property as a boolean.

property help

Report command line options.

More information on associated and general qualifiers can be found with -help -verbose

This property controls the addition of the -help switch, treat this property as a boolean.

property options

Prompt for standard and additional values.

If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

This property controls the addition of the -options switch, treat this property as a boolean.

property outfile

Output filename

This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

property pattern

Search pattern, using standard IUPAC one-letter codes

This controls the addition of the -pattern parameter and its associated value. Set this property to the argument value required.

property pmismatch

Number of mismatches

This controls the addition of the -pmismatch parameter and its associated value. Set this property to the argument value required.

property rformat

Specify the report format to output in.

This controls the addition of the -rformat parameter and its associated value. Set this property to the argument value required.

property sequence

Sequence database USA

This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.

property stdout

Write standard output.

This property controls the addition of the -stdout switch, treat this property as a boolean.

property verbose

Report some/full command line options

This property controls the addition of the -verbose switch, treat this property as a boolean.

property warning

Report warnings.

This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.Est2GenomeCommandline(cmd='est2genome', **kwargs)

Bases: Bio.Emboss.Applications._EmbossCommandLine

Commandline object for the est2genome program from EMBOSS.

__init__(self, cmd='est2genome', **kwargs)

Initialize the class.

property align

Show the alignment.

This controls the addition of the -align parameter and its associated value. Set this property to the argument value required.

property auto

Turn off prompts.

Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

This property controls the addition of the -auto switch, treat this property as a boolean.

property best

You can print out all comparisons instead of just the best

This controls the addition of the -best parameter and its associated value. Set this property to the argument value required.

property debug

Write debug output to program.dbg.

This property controls the addition of the -debug switch, treat this property as a boolean.

property die

Report dying program messages.

This property controls the addition of the -die switch, treat this property as a boolean.

property error

Report errors.

This property controls the addition of the -error switch, treat this property as a boolean.

property est

EST sequence(s)

This controls the addition of the -est parameter and its associated value. Set this property to the argument value required.

property filter

Read standard input, write standard output.

This property controls the addition of the -filter switch, treat this property as a boolean.

property gappenalty

Cost for deleting a single base in either sequence, excluding introns

This controls the addition of the -gappenalty parameter and its associated value. Set this property to the argument value required.

property genome

Genomic sequence

This controls the addition of the -genome parameter and its associated value. Set this property to the argument value required.

property help

Report command line options.

More information on associated and general qualifiers can be found with -help -verbose

This property controls the addition of the -help switch, treat this property as a boolean.

property intronpenalty

Cost for an intron, independent of length.

This controls the addition of the -intronpenalty parameter and its associated value. Set this property to the argument value required.

property match

Score for matching two bases

This controls the addition of the -match parameter and its associated value. Set this property to the argument value required.

property minscore

Exclude alignments with scores below this threshold score.

This controls the addition of the -minscore parameter and its associated value. Set this property to the argument value required.

property mismatch

Cost for mismatching two bases

This controls the addition of the -mismatch parameter and its associated value. Set this property to the argument value required.

property mode

This determines the comparion mode. ‘both’, ‘forward’ ‘reverse’

This controls the addition of the -mode parameter and its associated value. Set this property to the argument value required.

property options

Prompt for standard and additional values.

If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

This property controls the addition of the -options switch, treat this property as a boolean.

property outfile

Output filename

This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

property reverse

Reverse the orientation of the EST sequence

This controls the addition of the -reverse parameter and its associated value. Set this property to the argument value required.

property seed

Random number seed

This controls the addition of the -seed parameter and its associated value. Set this property to the argument value required.

property shuffle

Shuffle

This controls the addition of the -shuffle parameter and its associated value. Set this property to the argument value required.

property space

for linear-space recursion.

This controls the addition of the -space parameter and its associated value. Set this property to the argument value required.

property splice

Use donor and acceptor splice sites.

This controls the addition of the -splice parameter and its associated value. Set this property to the argument value required.

property splicepenalty

Cost for an intron, independent of length and starting/ending on donor-acceptor sites

This controls the addition of the -splicepenalty parameter and its associated value. Set this property to the argument value required.

property stdout

Write standard output.

This property controls the addition of the -stdout switch, treat this property as a boolean.

property verbose

Report some/full command line options

This property controls the addition of the -verbose switch, treat this property as a boolean.

property warning

Report warnings.

This property controls the addition of the -warning switch, treat this property as a boolean.

property width

Alignment width

This controls the addition of the -width parameter and its associated value. Set this property to the argument value required.

class Bio.Emboss.Applications.ETandemCommandline(cmd='etandem', **kwargs)

Bases: Bio.Emboss.Applications._EmbossCommandLine

Commandline object for the etandem program from EMBOSS.

__init__(self, cmd='etandem', **kwargs)

Initialize the class.

property auto

Turn off prompts.

Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

This property controls the addition of the -auto switch, treat this property as a boolean.

property debug

Write debug output to program.dbg.

This property controls the addition of the -debug switch, treat this property as a boolean.

property die

Report dying program messages.

This property controls the addition of the -die switch, treat this property as a boolean.

property error

Report errors.

This property controls the addition of the -error switch, treat this property as a boolean.

property filter

Read standard input, write standard output.

This property controls the addition of the -filter switch, treat this property as a boolean.

property help

Report command line options.

More information on associated and general qualifiers can be found with -help -verbose

This property controls the addition of the -help switch, treat this property as a boolean.

property maxrepeat

Maximum repeat size

This controls the addition of the -maxrepeat parameter and its associated value. Set this property to the argument value required.

property minrepeat

Minimum repeat size

This controls the addition of the -minrepeat parameter and its associated value. Set this property to the argument value required.

property mismatch

Allow N as a mismatch

This controls the addition of the -mismatch parameter and its associated value. Set this property to the argument value required.

property options

Prompt for standard and additional values.

If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

This property controls the addition of the -options switch, treat this property as a boolean.

property outfile

Output filename

This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

property rformat

Output report format

This controls the addition of the -rformat parameter and its associated value. Set this property to the argument value required.

property sequence

Sequence

This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.

property stdout

Write standard output.

This property controls the addition of the -stdout switch, treat this property as a boolean.

property threshold

Threshold score

This controls the addition of the -threshold parameter and its associated value. Set this property to the argument value required.

property uniform

Allow uniform consensus

This controls the addition of the -uniform parameter and its associated value. Set this property to the argument value required.

property verbose

Report some/full command line options

This property controls the addition of the -verbose switch, treat this property as a boolean.

property warning

Report warnings.

This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.EInvertedCommandline(cmd='einverted', **kwargs)

Bases: Bio.Emboss.Applications._EmbossCommandLine

Commandline object for the einverted program from EMBOSS.

__init__(self, cmd='einverted', **kwargs)

Initialize the class.

property auto

Turn off prompts.

Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

This property controls the addition of the -auto switch, treat this property as a boolean.

property debug

Write debug output to program.dbg.

This property controls the addition of the -debug switch, treat this property as a boolean.

property die

Report dying program messages.

This property controls the addition of the -die switch, treat this property as a boolean.

property error

Report errors.

This property controls the addition of the -error switch, treat this property as a boolean.

property filter

Read standard input, write standard output.

This property controls the addition of the -filter switch, treat this property as a boolean.

property gap

Gap penalty

This controls the addition of the -gap parameter and its associated value. Set this property to the argument value required.

property help

Report command line options.

More information on associated and general qualifiers can be found with -help -verbose

This property controls the addition of the -help switch, treat this property as a boolean.

property match

Match score

This controls the addition of the -match parameter and its associated value. Set this property to the argument value required.

property maxrepeat

Maximum separation between the start and end of repeat

This controls the addition of the -maxrepeat parameter and its associated value. Set this property to the argument value required.

property mismatch

Mismatch score

This controls the addition of the -mismatch parameter and its associated value. Set this property to the argument value required.

property options

Prompt for standard and additional values.

If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

This property controls the addition of the -options switch, treat this property as a boolean.

property outfile

Output filename

This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

property sequence

Sequence

This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.

property stdout

Write standard output.

This property controls the addition of the -stdout switch, treat this property as a boolean.

property threshold

Minimum score threshold

This controls the addition of the -threshold parameter and its associated value. Set this property to the argument value required.

property verbose

Report some/full command line options

This property controls the addition of the -verbose switch, treat this property as a boolean.

property warning

Report warnings.

This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.PalindromeCommandline(cmd='palindrome', **kwargs)

Bases: Bio.Emboss.Applications._EmbossCommandLine

Commandline object for the palindrome program from EMBOSS.

__init__(self, cmd='palindrome', **kwargs)

Initialize the class.

property auto

Turn off prompts.

Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

This property controls the addition of the -auto switch, treat this property as a boolean.

property debug

Write debug output to program.dbg.

This property controls the addition of the -debug switch, treat this property as a boolean.

property die

Report dying program messages.

This property controls the addition of the -die switch, treat this property as a boolean.

property error

Report errors.

This property controls the addition of the -error switch, treat this property as a boolean.

property filter

Read standard input, write standard output.

This property controls the addition of the -filter switch, treat this property as a boolean.

property gaplimit

Maximum gap between repeats

This controls the addition of the -gaplimit parameter and its associated value. Set this property to the argument value required.

property help

Report command line options.

More information on associated and general qualifiers can be found with -help -verbose

This property controls the addition of the -help switch, treat this property as a boolean.

property maxpallen

Maximum palindrome length

This controls the addition of the -maxpallen parameter and its associated value. Set this property to the argument value required.

property minpallen

Minimum palindrome length

This controls the addition of the -minpallen parameter and its associated value. Set this property to the argument value required.

property nummismatches

Number of mismatches allowed

This controls the addition of the -nummismatches parameter and its associated value. Set this property to the argument value required.

property options

Prompt for standard and additional values.

If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

This property controls the addition of the -options switch, treat this property as a boolean.

property outfile

Output filename

This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

property overlap

Report overlapping matches

This controls the addition of the -overlap parameter and its associated value. Set this property to the argument value required.

property sequence

Sequence

This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.

property stdout

Write standard output.

This property controls the addition of the -stdout switch, treat this property as a boolean.

property verbose

Report some/full command line options

This property controls the addition of the -verbose switch, treat this property as a boolean.

property warning

Report warnings.

This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.TranalignCommandline(cmd='tranalign', **kwargs)

Bases: Bio.Emboss.Applications._EmbossCommandLine

Commandline object for the tranalign program from EMBOSS.

__init__(self, cmd='tranalign', **kwargs)

Initialize the class.

property asequence

Nucleotide sequences to be aligned.

This controls the addition of the -asequence parameter and its associated value. Set this property to the argument value required.

property auto

Turn off prompts.

Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

This property controls the addition of the -auto switch, treat this property as a boolean.

property bsequence

Protein sequence alignment

This controls the addition of the -bsequence parameter and its associated value. Set this property to the argument value required.

property debug

Write debug output to program.dbg.

This property controls the addition of the -debug switch, treat this property as a boolean.

property die

Report dying program messages.

This property controls the addition of the -die switch, treat this property as a boolean.

property error

Report errors.

This property controls the addition of the -error switch, treat this property as a boolean.

property filter

Read standard input, write standard output.

This property controls the addition of the -filter switch, treat this property as a boolean.

property help

Report command line options.

More information on associated and general qualifiers can be found with -help -verbose

This property controls the addition of the -help switch, treat this property as a boolean.

property options

Prompt for standard and additional values.

If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

This property controls the addition of the -options switch, treat this property as a boolean.

property outfile

Output filename

This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

property outseq

Output sequence file.

This controls the addition of the -outseq parameter and its associated value. Set this property to the argument value required.

property stdout

Write standard output.

This property controls the addition of the -stdout switch, treat this property as a boolean.

property table

Code to use

This controls the addition of the -table parameter and its associated value. Set this property to the argument value required.

property verbose

Report some/full command line options

This property controls the addition of the -verbose switch, treat this property as a boolean.

property warning

Report warnings.

This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.DiffseqCommandline(cmd='diffseq', **kwargs)

Bases: Bio.Emboss.Applications._EmbossCommandLine

Commandline object for the diffseq program from EMBOSS.

__init__(self, cmd='diffseq', **kwargs)

Initialize the class.

property aoutfeat

File for output of first sequence’s features

This controls the addition of the -aoutfeat parameter and its associated value. Set this property to the argument value required.

property asequence

First sequence to compare

This controls the addition of the -asequence parameter and its associated value. Set this property to the argument value required.

property auto

Turn off prompts.

Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

This property controls the addition of the -auto switch, treat this property as a boolean.

property boutfeat

File for output of second sequence’s features

This controls the addition of the -boutfeat parameter and its associated value. Set this property to the argument value required.

property bsequence

Second sequence to compare

This controls the addition of the -bsequence parameter and its associated value. Set this property to the argument value required.

property debug

Write debug output to program.dbg.

This property controls the addition of the -debug switch, treat this property as a boolean.

property die

Report dying program messages.

This property controls the addition of the -die switch, treat this property as a boolean.

property error

Report errors.

This property controls the addition of the -error switch, treat this property as a boolean.

property filter

Read standard input, write standard output.

This property controls the addition of the -filter switch, treat this property as a boolean.

property help

Report command line options.

More information on associated and general qualifiers can be found with -help -verbose

This property controls the addition of the -help switch, treat this property as a boolean.

property options

Prompt for standard and additional values.

If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

This property controls the addition of the -options switch, treat this property as a boolean.

property outfile

Output filename

This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

property rformat

Output report file format

This controls the addition of the -rformat parameter and its associated value. Set this property to the argument value required.

property stdout

Write standard output.

This property controls the addition of the -stdout switch, treat this property as a boolean.

property verbose

Report some/full command line options

This property controls the addition of the -verbose switch, treat this property as a boolean.

property warning

Report warnings.

This property controls the addition of the -warning switch, treat this property as a boolean.

property wordsize

Word size to use for comparisons (10 default)

This controls the addition of the -wordsize parameter and its associated value. Set this property to the argument value required.

class Bio.Emboss.Applications.IepCommandline(cmd='iep', **kwargs)

Bases: Bio.Emboss.Applications._EmbossCommandLine

Commandline for EMBOSS iep: calculated isoelectric point and charge.

Examples

>>> from Bio.Emboss.Applications import IepCommandline
>>> iep_cline = IepCommandline(sequence="proteins.faa",
...                            outfile="proteins.txt")
>>> print(iep_cline)
iep -outfile=proteins.txt -sequence=proteins.faa

You would typically run the command line with iep_cline() or via the Python subprocess module, as described in the Biopython tutorial.

__init__(self, cmd='iep', **kwargs)

Initialize the class.

property amino

Number of N-termini

Integer 0 (default) or more.

This controls the addition of the -amino parameter and its associated value. Set this property to the argument value required.

property auto

Turn off prompts.

Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

This property controls the addition of the -auto switch, treat this property as a boolean.

property carboxyl

Number of C-termini

Integer 0 (default) or more.

This controls the addition of the -carboxyl parameter and its associated value. Set this property to the argument value required.

property debug

Write debug output to program.dbg.

This property controls the addition of the -debug switch, treat this property as a boolean.

property die

Report dying program messages.

This property controls the addition of the -die switch, treat this property as a boolean.

property disulphides

Number of disulphide bridges

Integer 0 (default) or more.

This controls the addition of the -disulphides parameter and its associated value. Set this property to the argument value required.

property error

Report errors.

This property controls the addition of the -error switch, treat this property as a boolean.

property filter

Read standard input, write standard output.

This property controls the addition of the -filter switch, treat this property as a boolean.

property help

Report command line options.

More information on associated and general qualifiers can be found with -help -verbose

This property controls the addition of the -help switch, treat this property as a boolean.

property lysinemodified

Number of modified lysines

Integer 0 (default) or more.

This controls the addition of the -lysinemodified parameter and its associated value. Set this property to the argument value required.

property notermini

Exclude (True) or include (False) charge at N and C terminus.

This controls the addition of the -notermini parameter and its associated value. Set this property to the argument value required.

property options

Prompt for standard and additional values.

If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

This property controls the addition of the -options switch, treat this property as a boolean.

property outfile

Output filename

This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

property sequence

Protein sequence(s) filename

This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.

property stdout

Write standard output.

This property controls the addition of the -stdout switch, treat this property as a boolean.

property verbose

Report some/full command line options

This property controls the addition of the -verbose switch, treat this property as a boolean.

property warning

Report warnings.

This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.SeqretCommandline(cmd='seqret', **kwargs)

Bases: Bio.Emboss.Applications._EmbossMinimalCommandLine

Commandline object for the seqret program from EMBOSS.

This tool allows you to interconvert between different sequence file formats (e.g. GenBank to FASTA). Combining Biopython’s Bio.SeqIO module with seqret using a suitable intermediate file format can allow you to read/write to an even wider range of file formats.

This wrapper currently only supports the core functionality, things like feature tables (in EMBOSS 6.1.0 onwards) are not yet included.

__init__(self, cmd='seqret', **kwargs)

Initialize the class.

property auto

Turn off prompts.

Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

This property controls the addition of the -auto switch, treat this property as a boolean.

property debug

Write debug output to program.dbg.

This property controls the addition of the -debug switch, treat this property as a boolean.

property die

Report dying program messages.

This property controls the addition of the -die switch, treat this property as a boolean.

property error

Report errors.

This property controls the addition of the -error switch, treat this property as a boolean.

property filter

Read standard input, write standard output.

This property controls the addition of the -filter switch, treat this property as a boolean.

property help

Report command line options.

More information on associated and general qualifiers can be found with -help -verbose

This property controls the addition of the -help switch, treat this property as a boolean.

property options

Prompt for standard and additional values.

If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

This property controls the addition of the -options switch, treat this property as a boolean.

property osformat

Output sequence(s) format (e.g. fasta, genbank)

This controls the addition of the -osformat parameter and its associated value. Set this property to the argument value required.

property outseq

Output sequence file.

This controls the addition of the -outseq parameter and its associated value. Set this property to the argument value required.

property sequence

Input sequence(s) filename

This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.

property sformat

Input sequence(s) format (e.g. fasta, genbank)

This controls the addition of the -sformat parameter and its associated value. Set this property to the argument value required.

property stdout

Write standard output.

This property controls the addition of the -stdout switch, treat this property as a boolean.

property verbose

Report some/full command line options

This property controls the addition of the -verbose switch, treat this property as a boolean.

property warning

Report warnings.

This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.SeqmatchallCommandline(cmd='seqmatchall', **kwargs)

Bases: Bio.Emboss.Applications._EmbossCommandLine

Commandline object for the seqmatchall program from EMBOSS.

e.g. >>> cline = SeqmatchallCommandline(sequence=”opuntia.fasta”, outfile=”opuntia.txt”) >>> cline.auto = True >>> cline.wordsize = 18 >>> cline.aformat = “pair” >>> print(cline) seqmatchall -auto -outfile=opuntia.txt -sequence=opuntia.fasta -wordsize=18 -aformat=pair

__init__(self, cmd='seqmatchall', **kwargs)

Initialize the class.

property aformat

Display output in a different specified output format

This controls the addition of the -aformat parameter and its associated value. Set this property to the argument value required.

property auto

Turn off prompts.

Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

This property controls the addition of the -auto switch, treat this property as a boolean.

property debug

Write debug output to program.dbg.

This property controls the addition of the -debug switch, treat this property as a boolean.

property die

Report dying program messages.

This property controls the addition of the -die switch, treat this property as a boolean.

property error

Report errors.

This property controls the addition of the -error switch, treat this property as a boolean.

property filter

Read standard input, write standard output.

This property controls the addition of the -filter switch, treat this property as a boolean.

property help

Report command line options.

More information on associated and general qualifiers can be found with -help -verbose

This property controls the addition of the -help switch, treat this property as a boolean.

property options

Prompt for standard and additional values.

If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

This property controls the addition of the -options switch, treat this property as a boolean.

property outfile

Output filename

This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

property sequence

Readable set of sequences

This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.

property stdout

Write standard output.

This property controls the addition of the -stdout switch, treat this property as a boolean.

property verbose

Report some/full command line options

This property controls the addition of the -verbose switch, treat this property as a boolean.

property warning

Report warnings.

This property controls the addition of the -warning switch, treat this property as a boolean.

property wordsize

Word size (Integer 2 or more, default 4)

This controls the addition of the -wordsize parameter and its associated value. Set this property to the argument value required.