Bio.Emboss.Applications module¶
Code to interact with and run various EMBOSS programs.
These classes follow the AbstractCommandline interfaces for running programs.
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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:
>>> 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
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__init__
(self, cmd='eprimer3', **kwargs)¶ Initialize the class.
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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.
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property
debug
¶ Write debug output to program.dbg.
This property controls the addition of the -debug switch, treat this property as a boolean.
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property
die
¶ Report dying program messages.
This property controls the addition of the -die switch, treat this property as a boolean.
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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.
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property
error
¶ Report errors.
This property controls the addition of the -error switch, treat this property as a boolean.
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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.
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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.
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property
filter
¶ Read standard input, write standard output.
This property controls the addition of the -filter switch, treat this property as a boolean.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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property
mishyblibraryfile
¶ Library file of seqs to avoid internal oligo hybridisation.
This controls the addition of the -mishyblibraryfile parameter and its associated value. Set this property to the argument value required.
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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.
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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.
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property
oanyself
¶ Maximum allowable alignment score for self-complementarity.
This controls the addition of the -oanyself parameter and its associated value. Set this property to the argument value required.
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property
odnaconc
¶ Nanomolar concentration of internal oligo in the hybridisation.
This controls the addition of the -odnaconc parameter and its associated value. Set this property to the argument value required.
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property
oendself
¶ Max 3’-anchored self-complementarity global alignment score.
This controls the addition of the -oendself parameter and its associated value. Set this property to the argument value required.
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property
oexcludedregion
¶ Do not pick internal oligos in this region.
This controls the addition of the -oexcludedregion parameter and its associated value. Set this property to the argument value required.
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property
ogcmax
¶ Maximum GC% for internal oligo.
This controls the addition of the -ogcmax parameter and its associated value. Set this property to the argument value required.
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property
ogcmin
¶ Minimum GC% for internal oligo.
This controls the addition of the -ogcmin parameter and its associated value. Set this property to the argument value required.
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property
ogcopt
¶ Optimum GC% for internal oligo.
This controls the addition of the -ogcopt parameter and its associated value. Set this property to the argument value required.
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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.
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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.
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property
omaxsize
¶ Maximum length of internal oligo.
This controls the addition of the -omaxsize parameter and its associated value. Set this property to the argument value required.
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property
ominsize
¶ Minimum length of internal oligo.
This controls the addition of the -ominsize parameter and its associated value. Set this property to the argument value required.
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property
omishybmax
¶ Maximum alignment score for hybridisation of internal oligo to library specified by -mishyblibraryfile.
This controls the addition of the -omishybmax parameter and its associated value. Set this property to the argument value required.
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property
opolyxmax
¶ Maximum length of mononucleotide repeat in internal oligo.
This controls the addition of the -opolyxmax parameter and its associated value. Set this property to the argument value required.
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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.
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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.
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property
osaltconc
¶ Millimolar concentration of salt in the hybridisation.
This controls the addition of the -osaltconc parameter and its associated value. Set this property to the argument value required.
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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.
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property
osizeopt
¶ Optimum length of internal oligo.
This controls the addition of the -osizeopt parameter and its associated value. Set this property to the argument value required.
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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.
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property
otmmax
¶ Maximum melting temperature of internal oligo.
This controls the addition of the -otmmax parameter and its associated value. Set this property to the argument value required.
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property
otmmin
¶ Minimum melting temperature of internal oligo.
This controls the addition of the -otmmin parameter and its associated value. Set this property to the argument value required.
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property
otmopt
¶ Optimum melting temperature of internal oligo.
This controls the addition of the -otmopt parameter and its associated value. Set this property to the argument value required.
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property
outfile
¶ Output filename
This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.
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property
prange
¶ Acceptable range of length for the PCR product.
This controls the addition of the -prange parameter and its associated value. Set this property to the argument value required.
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property
psizeopt
¶ Optimum size for the PCR product.
This controls the addition of the -psizeopt parameter and its associated value. Set this property to the argument value required.
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property
ptmmax
¶ Maximum allowed melting temperature for the amplicon.
This controls the addition of the -ptmmax parameter and its associated value. Set this property to the argument value required.
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property
ptmmin
¶ Minimum allowed melting temperature for the amplicon.
This controls the addition of the -ptmmin parameter and its associated value. Set this property to the argument value required.
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property
ptmopt
¶ Optimum melting temperature for the PCR product.
This controls the addition of the -ptmopt parameter and its associated value. Set this property to the argument value required.
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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.
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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.
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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.
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property
stdout
¶ Write standard output.
This property controls the addition of the -stdout switch, treat this property as a boolean.
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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.
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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.
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property
verbose
¶ Report some/full command line options
This property controls the addition of the -verbose switch, treat this property as a boolean.
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property
warning
¶ Report warnings.
This property controls the addition of the -warning switch, treat this property as a boolean.
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class
Bio.Emboss.Applications.
PrimerSearchCommandline
(cmd='primersearch', **kwargs)¶ Bases:
Bio.Emboss.Applications._EmbossCommandLine
Commandline object for the primersearch program from EMBOSS.
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__init__
(self, cmd='primersearch', **kwargs)¶ Initialize the class.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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property
outfile
¶ Output filename
This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.
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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.
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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.
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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.
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property
stdout
¶ Write standard output.
This property controls the addition of the -stdout switch, treat this property as a boolean.
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property
verbose
¶ Report some/full command line options
This property controls the addition of the -verbose switch, treat this property as a boolean.
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property
warning
¶ Report warnings.
This property controls the addition of the -warning switch, treat this property as a boolean.
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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.
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__init__
(self, cmd='fdnadist', **kwargs)¶ Initialize the class.
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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.
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property
basefreq
¶ specify basefreqs
This controls the addition of the -basefreq parameter and its associated value. Set this property to the argument value required.
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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.
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property
debug
¶ Write debug output to program.dbg.
This property controls the addition of the -debug switch, treat this property as a boolean.
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property
die
¶ Report dying program messages.
This property controls the addition of the -die switch, treat this property as a boolean.
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property
error
¶ Report errors.
This property controls the addition of the -error switch, treat this property as a boolean.
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property
filter
¶ Read standard input, write standard output.
This property controls the addition of the -filter switch, treat this property as a boolean.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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property
outfile
¶ Output filename
This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.
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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.
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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.
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property
stdout
¶ Write standard output.
This property controls the addition of the -stdout switch, treat this property as a boolean.
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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.
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property
verbose
¶ Report some/full command line options
This property controls the addition of the -verbose switch, treat this property as a boolean.
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property
warning
¶ Report warnings.
This property controls the addition of the -warning switch, treat this property as a boolean.
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property
weights
¶ weights file
This controls the addition of the -weights parameter and its associated value. Set this property to the argument value required.
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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.
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__init__
(self, cmd='ftreedist', **kwargs)¶ Initialize the class.
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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.
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property
debug
¶ Write debug output to program.dbg.
This property controls the addition of the -debug switch, treat this property as a boolean.
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property
die
¶ Report dying program messages.
This property controls the addition of the -die switch, treat this property as a boolean.
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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.
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property
error
¶ Report errors.
This property controls the addition of the -error switch, treat this property as a boolean.
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property
filter
¶ Read standard input, write standard output.
This property controls the addition of the -filter switch, treat this property as a boolean.
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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.
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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.
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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.
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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.
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property
outfile
¶ Output filename
This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.
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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.
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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.
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property
stdout
¶ Write standard output.
This property controls the addition of the -stdout switch, treat this property as a boolean.
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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.
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property
verbose
¶ Report some/full command line options
This property controls the addition of the -verbose switch, treat this property as a boolean.
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property
warning
¶ Report warnings.
This property controls the addition of the -warning switch, treat this property as a boolean.
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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.
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__init__
(self, cmd='fneighbor', **kwargs)¶ Initialize the class.
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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.
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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.
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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.
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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.
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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.
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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.
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property
outfile
¶ Output filename
This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.
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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.
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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.
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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.
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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.
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property
stdout
¶ Write standard output.
This property controls the addition of the -stdout switch, treat this property as a boolean.
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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.
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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.
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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.
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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.
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__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.
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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.
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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.
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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.
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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’, or ‘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.
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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.
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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.
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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.
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property
debug
¶ Write debug output to program.dbg.
This property controls the addition of the -debug switch, treat this property as a boolean.
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property
die
¶ Report dying program messages.
This property controls the addition of the -die switch, treat this property as a boolean.
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property
error
¶ Report errors.
This property controls the addition of the -error switch, treat this property as a boolean.
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property
filter
¶ Read standard input, write standard output.
This property controls the addition of the -filter switch, treat this property as a boolean.
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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.
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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.
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property
outfile
¶ Output filename
This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.
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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.
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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.
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property
warning
¶ Report warnings.
This property controls the addition of the -warning switch, treat this property as a boolean.
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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.
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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.
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__init__
(self, cmd='iep', **kwargs)¶ Initialize the class.
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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.
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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.
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property
debug
¶ Write debug output to program.dbg.
This property controls the addition of the -debug switch, treat this property as a boolean.
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property
die
¶ Report dying program messages.
This property controls the addition of the -die switch, treat this property as a boolean.
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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.
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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.
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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.
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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.
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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.
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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.
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property
outfile
¶ Output filename
This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.
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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.
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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.
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property
warning
¶ Report warnings.
This property controls the addition of the -warning switch, treat this property as a boolean.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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
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__init__
(self, cmd='seqmatchall', **kwargs)¶ Initialize the class.
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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.
-