Bio.Emboss.Applications module
Code to interact with and run various EMBOSS programs (OBSOLETE).
These classes follow the AbstractCommandline interfaces for running programs.
We have decided to remove this module in future, and instead recommend building your command and invoking it via the subprocess module directly.
- class Bio.Emboss.Applications.Primer3Commandline(cmd='eprimer3', **kwargs)
Bases:
_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
- __init__(cmd='eprimer3', **kwargs)
Initialize the class.
- property auto
Turn off prompts.
Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.
This property controls the addition of the -auto switch, treat this property as a boolean.
- property debug
Write debug output to program.dbg.
This property controls the addition of the -debug switch, treat this property as a boolean.
- property die
Report dying program messages.
This property controls the addition of the -die switch, treat this property as a boolean.
- property dnaconc
Nanomolar concentration of annealing oligos in the PCR.
This controls the addition of the -dnaconc parameter and its associated value. Set this property to the argument value required.
- property error
Report errors.
This property controls the addition of the -error switch, treat this property as a boolean.
- property excludedregion
Regions to exclude from primer picking.
This controls the addition of the -excludedregion parameter and its associated value. Set this property to the argument value required.
- property explainflag
Produce output tags with eprimer3 statistics
This controls the addition of the -explainflag parameter and its associated value. Set this property to the argument value required.
- property filter
Read standard input, write standard output.
This property controls the addition of the -filter switch, treat this property as a boolean.
- property forwardinput
Sequence of a forward primer to check.
This controls the addition of the -forwardinput parameter and its associated value. Set this property to the argument value required.
- property gcclamp
The required number of Gs and Cs at the 3’ of each primer.
This controls the addition of the -gcclamp parameter and its associated value. Set this property to the argument value required.
- property help
Report command line options.
More information on associated and general qualifiers can be found with -help -verbose
This property controls the addition of the -help switch, treat this property as a boolean.
- property hybridprobe
Find an internal oligo to use as a hyb probe.
This controls the addition of the -hybridprobe parameter and its associated value. Set this property to the argument value required.
- property includedregion
Subregion of the sequence in which to pick primers.
This controls the addition of the -includedregion parameter and its associated value. Set this property to the argument value required.
- property maxdifftm
Maximum difference in melting temperatures between forward and reverse primers.
This controls the addition of the -maxdifftm parameter and its associated value. Set this property to the argument value required.
- property maxgc
Maximum GC% for a primer.
This controls the addition of the -maxgc parameter and its associated value. Set this property to the argument value required.
- property maxmispriming
Maximum allowed similarity of primers to sequences in library specified by -mispriminglibrary
This controls the addition of the -maxmispriming parameter and its associated value. Set this property to the argument value required.
- property maxpolyx
Maximum allowable mononucleotide repeat length in a primer.
This controls the addition of the -maxpolyx parameter and its associated value. Set this property to the argument value required.
- property maxsize
Maximum length of a primer oligo.
This controls the addition of the -maxsize parameter and its associated value. Set this property to the argument value required.
- property maxtm
Maximum melting temperature for a primer oligo.
This controls the addition of the -maxtm parameter and its associated value. Set this property to the argument value required.
- property mingc
Minimum GC% for a primer.
This controls the addition of the -mingc parameter and its associated value. Set this property to the argument value required.
- property minsize
Minimum length of a primer oligo.
This controls the addition of the -minsize parameter and its associated value. Set this property to the argument value required.
- property mintm
Minimum melting temperature for a primer oligo.
This controls the addition of the -mintm parameter and its associated value. Set this property to the argument value required.
- property mishyblibraryfile
Library file of seqs to avoid internal oligo hybridisation.
This controls the addition of the -mishyblibraryfile parameter and its associated value. Set this property to the argument value required.
- property mispriminglibraryfile
File containing library of sequences to avoid amplifying
This controls the addition of the -mispriminglibraryfile parameter and its associated value. Set this property to the argument value required.
- property numreturn
Maximum number of primer pairs to return.
This controls the addition of the -numreturn parameter and its associated value. Set this property to the argument value required.
- property oanyself
Maximum allowable alignment score for self-complementarity.
This controls the addition of the -oanyself parameter and its associated value. Set this property to the argument value required.
- property odnaconc
Nanomolar concentration of internal oligo in the hybridisation.
This controls the addition of the -odnaconc parameter and its associated value. Set this property to the argument value required.
- property oendself
Max 3’-anchored self-complementarity global alignment score.
This controls the addition of the -oendself parameter and its associated value. Set this property to the argument value required.
- property oexcludedregion
Do not pick internal oligos in this region.
This controls the addition of the -oexcludedregion parameter and its associated value. Set this property to the argument value required.
- property ogcmax
Maximum GC% for internal oligo.
This controls the addition of the -ogcmax parameter and its associated value. Set this property to the argument value required.
- property ogcmin
Minimum GC% for internal oligo.
This controls the addition of the -ogcmin parameter and its associated value. Set this property to the argument value required.
- property ogcopt
Optimum GC% for internal oligo.
This controls the addition of the -ogcopt parameter and its associated value. Set this property to the argument value required.
- property ogcpercent
Optimum GC% for a primer.
This controls the addition of the -ogcpercent parameter and its associated value. Set this property to the argument value required.
- property oligoinput
Sequence of the internal oligo.
This controls the addition of the -oligoinput parameter and its associated value. Set this property to the argument value required.
- property 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.
- 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.
- 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.
- 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.
- property options
Prompt for standard and additional values.
If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.
This property controls the addition of the -options switch, treat this property as a boolean.
- property opttm
Optimum melting temperature for a primer oligo.
Option added in EMBOSS 6.6.0, replacing -otm
This controls the addition of the -opttm parameter and its associated value. Set this property to the argument value required.
- property osaltconc
Millimolar concentration of salt in the hybridisation.
This controls the addition of the -osaltconc parameter and its associated value. Set this property to the argument value required.
- property osize
Optimum length of a primer oligo.
This controls the addition of the -osize parameter and its associated value. Set this property to the argument value required.
- property osizeopt
Optimum length of internal oligo.
This controls the addition of the -osizeopt parameter and its associated value. Set this property to the argument value required.
- property otm
Melting temperature for primer oligo (OBSOLETE).
Option replaced in EMBOSS 6.6.0 by -opttm
This controls the addition of the -otm parameter and its associated value. Set this property to the argument value required.
- property otmmax
Maximum melting temperature of internal oligo.
This controls the addition of the -otmmax parameter and its associated value. Set this property to the argument value required.
- property otmmin
Minimum melting temperature of internal oligo.
This controls the addition of the -otmmin parameter and its associated value. Set this property to the argument value required.
- property otmopt
Optimum melting temperature of internal oligo.
This controls the addition of the -otmopt parameter and its associated value. Set this property to the argument value required.
- property outfile
Output filename
This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.
- property prange
Acceptable range of length for the PCR product.
This controls the addition of the -prange parameter and its associated value. Set this property to the argument value required.
- 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.
- 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.
- 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.
- 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.
- property reverseinput
Sequence of a reverse primer to check.
This controls the addition of the -reverseinput parameter and its associated value. Set this property to the argument value required.
- property saltconc
Millimolar salt concentration in the PCR.
This controls the addition of the -saltconc parameter and its associated value. Set this property to the argument value required.
- property sequence
Sequence to choose primers from.
This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.
- property stdout
Write standard output.
This property controls the addition of the -stdout switch, treat this property as a boolean.
- property target
Sequence to target for flanking primers.
This controls the addition of the -target parameter and its associated value. Set this property to the argument value required.
- property task
Tell eprimer3 what task to perform.
This controls the addition of the -task parameter and its associated value. Set this property to the argument value required.
- property verbose
Report some/full command line options
This property controls the addition of the -verbose switch, treat this property as a boolean.
- property warning
Report warnings.
This property controls the addition of the -warning switch, treat this property as a boolean.
- class Bio.Emboss.Applications.PrimerSearchCommandline(cmd='primersearch', **kwargs)
Bases:
_EmbossCommandLine
Commandline object for the primersearch program from EMBOSS.
- __init__(cmd='primersearch', **kwargs)
Initialize the class.
- property auto
Turn off prompts.
Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.
This property controls the addition of the -auto switch, treat this property as a boolean.
- property debug
Write debug output to program.dbg.
This property controls the addition of the -debug switch, treat this property as a boolean.
- property die
Report dying program messages.
This property controls the addition of the -die switch, treat this property as a boolean.
- property error
Report errors.
This property controls the addition of the -error switch, treat this property as a boolean.
- property filter
Read standard input, write standard output.
This property controls the addition of the -filter switch, treat this property as a boolean.
- property help
Report command line options.
More information on associated and general qualifiers can be found with -help -verbose
This property controls the addition of the -help switch, treat this property as a boolean.
- property infile
File containing the primer pairs to search for.
This controls the addition of the -infile parameter and its associated value. Set this property to the argument value required.
- property mismatchpercent
Allowed percentage mismatch (any integer value, default 0).
This controls the addition of the -mismatchpercent parameter and its associated value. Set this property to the argument value required.
- property options
Prompt for standard and additional values.
If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.
This property controls the addition of the -options switch, treat this property as a boolean.
- property outfile
Output filename
This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.
- property seqall
Sequence to look for the primer pairs in.
This controls the addition of the -seqall parameter and its associated value. Set this property to the argument value required.
- property snucleotide
Sequences are nucleotide (boolean)
This controls the addition of the -snucleotide parameter and its associated value. Set this property to the argument value required.
- property sprotein
Sequences are protein (boolean)
This controls the addition of the -sprotein parameter and its associated value. Set this property to the argument value required.
- property stdout
Write standard output.
This property controls the addition of the -stdout switch, treat this property as a boolean.
- property verbose
Report some/full command line options
This property controls the addition of the -verbose switch, treat this property as a boolean.
- property warning
Report warnings.
This property controls the addition of the -warning switch, treat this property as a boolean.
- class Bio.Emboss.Applications.FDNADistCommandline(cmd='fdnadist', **kwargs)
Bases:
_EmbossCommandLine
Commandline object for the fdnadist program from EMBOSS.
fdnadist is an EMBOSS wrapper for the PHYLIP program dnadist for calculating distance matrices from DNA sequence files.
- __init__(cmd='fdnadist', **kwargs)
Initialize the class.
- property auto
Turn off prompts.
Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.
This property controls the addition of the -auto switch, treat this property as a boolean.
- property basefreq
specify basefreqs
This controls the addition of the -basefreq parameter and its associated value. Set this property to the argument value required.
- property categories
File of substitution rate categories
This controls the addition of the -categories parameter and its associated value. Set this property to the argument value required.
- property debug
Write debug output to program.dbg.
This property controls the addition of the -debug switch, treat this property as a boolean.
- property die
Report dying program messages.
This property controls the addition of the -die switch, treat this property as a boolean.
- property error
Report errors.
This property controls the addition of the -error switch, treat this property as a boolean.
- property filter
Read standard input, write standard output.
This property controls the addition of the -filter switch, treat this property as a boolean.
- property freqsfrom
use empirical base freqs
This controls the addition of the -freqsfrom parameter and its associated value. Set this property to the argument value required.
- property gamma
This controls the addition of the -gamma parameter and its associated value. Set this property to the argument value required.
- property gammacoefficient
value for gamma (> 0.001)
This controls the addition of the -gammacoefficient parameter and its associated value. Set this property to the argument value required.
- property help
Report command line options.
More information on associated and general qualifiers can be found with -help -verbose
This property controls the addition of the -help switch, treat this property as a boolean.
- property invarfrac
proportoin of invariant sites
This controls the addition of the -invarfrac parameter and its associated value. Set this property to the argument value required.
- property lower
lower triangle matrix (y/N)
This controls the addition of the -lower parameter and its associated value. Set this property to the argument value required.
- property method
sub. model [f,k,j,l,s]
This controls the addition of the -method parameter and its associated value. Set this property to the argument value required.
- property ncategories
number of rate categories (1-9)
This controls the addition of the -ncategories parameter and its associated value. Set this property to the argument value required.
- property options
Prompt for standard and additional values.
If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.
This property controls the addition of the -options switch, treat this property as a boolean.
- property outfile
Output filename
This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.
- property rate
rate for each category
This controls the addition of the -rate parameter and its associated value. Set this property to the argument value required.
- property sequence
seq file to use (phylip)
This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.
- property stdout
Write standard output.
This property controls the addition of the -stdout switch, treat this property as a boolean.
- property ttratio
ts/tv ratio
This controls the addition of the -ttratio parameter and its associated value. Set this property to the argument value required.
- property verbose
Report some/full command line options
This property controls the addition of the -verbose switch, treat this property as a boolean.
- property warning
Report warnings.
This property controls the addition of the -warning switch, treat this property as a boolean.
- property weights
weights file
This controls the addition of the -weights parameter and its associated value. Set this property to the argument value required.
- class Bio.Emboss.Applications.FTreeDistCommandline(cmd='ftreedist', **kwargs)
Bases:
_EmbossCommandLine
Commandline object for the ftreedist program from EMBOSS.
ftreedist is an EMBOSS wrapper for the PHYLIP program treedist used for calculating distance measures between phylogentic trees.
- __init__(cmd='ftreedist', **kwargs)
Initialize the class.
- property auto
Turn off prompts.
Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.
This property controls the addition of the -auto switch, treat this property as a boolean.
- property debug
Write debug output to program.dbg.
This property controls the addition of the -debug switch, treat this property as a boolean.
- property die
Report dying program messages.
This property controls the addition of the -die switch, treat this property as a boolean.
- property dtype
distance type ([S]ymetric, [b]ranch score)
This controls the addition of the -dtype parameter and its associated value. Set this property to the argument value required.
- property error
Report errors.
This property controls the addition of the -error switch, treat this property as a boolean.
- property filter
Read standard input, write standard output.
This property controls the addition of the -filter switch, treat this property as a boolean.
- property help
Report command line options.
More information on associated and general qualifiers can be found with -help -verbose
This property controls the addition of the -help switch, treat this property as a boolean.
- property intreefile
tree file to score (phylip)
This controls the addition of the -intreefile parameter and its associated value. Set this property to the argument value required.
- property noroot
treat trees as rooted [N/y]
This controls the addition of the -noroot parameter and its associated value. Set this property to the argument value required.
- property options
Prompt for standard and additional values.
If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.
This property controls the addition of the -options switch, treat this property as a boolean.
- property outfile
Output filename
This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.
- property outgrno
which taxon to root the trees with (starts from 0)
This controls the addition of the -outgrno parameter and its associated value. Set this property to the argument value required.
- property pairing
tree pairing method ([A]djacent pairs, all [p]ossible pairs)
This controls the addition of the -pairing parameter and its associated value. Set this property to the argument value required.
- property stdout
Write standard output.
This property controls the addition of the -stdout switch, treat this property as a boolean.
- property style
output style - [V]erbose, [f]ill, [s]parse
This controls the addition of the -style parameter and its associated value. Set this property to the argument value required.
- property verbose
Report some/full command line options
This property controls the addition of the -verbose switch, treat this property as a boolean.
- property warning
Report warnings.
This property controls the addition of the -warning switch, treat this property as a boolean.
- class Bio.Emboss.Applications.FNeighborCommandline(cmd='fneighbor', **kwargs)
Bases:
_EmbossCommandLine
Commandline object for the fneighbor program from EMBOSS.
fneighbor is an EMBOSS wrapper for the PHYLIP program neighbor used for calculating neighbor-joining or UPGMA trees from distance matrices.
- __init__(cmd='fneighbor', **kwargs)
Initialize the class.
- property auto
Turn off prompts.
Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.
This property controls the addition of the -auto switch, treat this property as a boolean.
- property datafile
dist file to use (phylip)
This controls the addition of the -datafile parameter and its associated value. Set this property to the argument value required.
- property debug
Write debug output to program.dbg.
This property controls the addition of the -debug switch, treat this property as a boolean.
- property die
Report dying program messages.
This property controls the addition of the -die switch, treat this property as a boolean.
- property error
Report errors.
This property controls the addition of the -error switch, treat this property as a boolean.
- property filter
Read standard input, write standard output.
This property controls the addition of the -filter switch, treat this property as a boolean.
- property help
Report command line options.
More information on associated and general qualifiers can be found with -help -verbose
This property controls the addition of the -help switch, treat this property as a boolean.
- property jumble
randommise input order (Y/n)
This controls the addition of the -jumble parameter and its associated value. Set this property to the argument value required.
- property matrixtype
is matrix square (S), upper (U) or lower (L)
This controls the addition of the -matrixtype parameter and its associated value. Set this property to the argument value required.
- property options
Prompt for standard and additional values.
If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.
This property controls the addition of the -options switch, treat this property as a boolean.
- property outfile
Output filename
This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.
- property outgrno
taxon to use as OG
This controls the addition of the -outgrno parameter and its associated value. Set this property to the argument value required.
- property outtreefile
filename for output tree
This controls the addition of the -outtreefile parameter and its associated value. Set this property to the argument value required.
- property progress
print progress (Y/n)
This controls the addition of the -progress parameter and its associated value. Set this property to the argument value required.
- property seed
provide a random seed
This controls the addition of the -seed parameter and its associated value. Set this property to the argument value required.
- property stdout
Write standard output.
This property controls the addition of the -stdout switch, treat this property as a boolean.
- property treeprint
print tree (Y/n)
This controls the addition of the -treeprint parameter and its associated value. Set this property to the argument value required.
- property treetype
nj or UPGMA tree (n/u)
This controls the addition of the -treetype parameter and its associated value. Set this property to the argument value required.
- property trout
write tree (Y/n)
This controls the addition of the -trout parameter and its associated value. Set this property to the argument value required.
- property verbose
Report some/full command line options
This property controls the addition of the -verbose switch, treat this property as a boolean.
- property warning
Report warnings.
This property controls the addition of the -warning switch, treat this property as a boolean.
- class Bio.Emboss.Applications.FSeqBootCommandline(cmd='fseqboot', **kwargs)
Bases:
_EmbossCommandLine
Commandline object for the fseqboot program from EMBOSS.
fseqboot is an EMBOSS wrapper for the PHYLIP program seqboot used to pseudo-sample alignment files.
- __init__(cmd='fseqboot', **kwargs)
Initialize the class.
- property auto
Turn off prompts.
Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.
This property controls the addition of the -auto switch, treat this property as a boolean.
- property blocksize
print progress (Y/n)
This controls the addition of the -blocksize parameter and its associated value. Set this property to the argument value required.
- property catergories
file of input categories
This controls the addition of the -categories parameter and its associated value. Set this property to the argument value required.
- property debug
Write debug output to program.dbg.
This property controls the addition of the -debug switch, treat this property as a boolean.
- property die
Report dying program messages.
This property controls the addition of the -die switch, treat this property as a boolean.
- property dotdiff
Use dot-differencing? [Y/n]
This controls the addition of the -dotdiff parameter and its associated value. Set this property to the argument value required.
- property error
Report errors.
This property controls the addition of the -error switch, treat this property as a boolean.
- property filter
Read standard input, write standard output.
This property controls the addition of the -filter switch, treat this property as a boolean.
- property fracsample
fraction to resample
This controls the addition of the -fracsample parameter and its associated value. Set this property to the argument value required.
- property help
Report command line options.
More information on associated and general qualifiers can be found with -help -verbose
This property controls the addition of the -help switch, treat this property as a boolean.
- property jusweights
what to write out [D]atasets of just [w]eights
This controls the addition of the -justweights parameter and its associated value. Set this property to the argument value required.
- property options
Prompt for standard and additional values.
If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.
This property controls the addition of the -options switch, treat this property as a boolean.
- property outfile
Output filename
This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.
- property regular
absolute number to resample
This controls the addition of the -regular parameter and its associated value. Set this property to the argument value required.
- property reps
how many replicates, defaults to 100)
This controls the addition of the -reps parameter and its associated value. Set this property to the argument value required.
- property rewriteformat
output format ([P]hyilp, [n]exus, [x]ml
This controls the addition of the -rewriteformat parameter and its associated value. Set this property to the argument value required.
- property seed
specify random seed
This controls the addition of the -seed parameter and its associated value. Set this property to the argument value required.
- property seqtype
output format ([D]na, [p]rotein, [r]na
This controls the addition of the -seqtype parameter and its associated value. Set this property to the argument value required.
- property sequence
seq file to sample (phylip)
This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.
- property stdout
Write standard output.
This property controls the addition of the -stdout switch, treat this property as a boolean.
- property test
specify operation, default is bootstrap
This controls the addition of the -test parameter and its associated value. Set this property to the argument value required.
- property verbose
Report some/full command line options
This property controls the addition of the -verbose switch, treat this property as a boolean.
- property warning
Report warnings.
This property controls the addition of the -warning switch, treat this property as a boolean.
- property weights
weights file
This controls the addition of the -weights parameter and its associated value. Set this property to the argument value required.
- class Bio.Emboss.Applications.FDNAParsCommandline(cmd='fdnapars', **kwargs)
Bases:
_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__(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:
_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__(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:
_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__(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 category (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
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 categories (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:
_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__(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:
_EmbossCommandLine
Commandline object for the water program from EMBOSS.
- __init__(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:
_EmbossCommandLine
Commandline object for the needle program from EMBOSS.
- __init__(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 penalty 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:
_EmbossCommandLine
Commandline object for the needleall program from EMBOSS.
- __init__(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 penalty 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:
_EmbossCommandLine
Commandline object for the stretcher program from EMBOSS.
- __init__(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:
_EmbossCommandLine
Commandline object for the fuzznuc program from EMBOSS.
- __init__(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:
_EmbossCommandLine
Commandline object for the fuzzpro program from EMBOSS.
- __init__(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:
_EmbossCommandLine
Commandline object for the est2genome program from EMBOSS.
- __init__(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 comparison 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:
_EmbossCommandLine
Commandline object for the etandem program from EMBOSS.
- __init__(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:
_EmbossCommandLine
Commandline object for the einverted program from EMBOSS.
- __init__(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:
_EmbossCommandLine
Commandline object for the palindrome program from EMBOSS.
- __init__(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:
_EmbossCommandLine
Commandline object for the tranalign program from EMBOSS.
- __init__(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:
_EmbossCommandLine
Commandline object for the diffseq program from EMBOSS.
- __init__(cmd='diffseq', **kwargs)
Initialize the class.
- property aoutfeat
File for output of first sequence’s features
This controls the addition of the -aoutfeat parameter and its associated value. Set this property to the argument value required.
- property asequence
First sequence to compare
This controls the addition of the -asequence parameter and its associated value. Set this property to the argument value required.
- property auto
Turn off prompts.
Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.
This property controls the addition of the -auto switch, treat this property as a boolean.
- property boutfeat
File for output of second sequence’s features
This controls the addition of the -boutfeat parameter and its associated value. Set this property to the argument value required.
- property bsequence
Second sequence to compare
This controls the addition of the -bsequence parameter and its associated value. Set this property to the argument value required.
- property debug
Write debug output to program.dbg.
This property controls the addition of the -debug switch, treat this property as a boolean.
- property die
Report dying program messages.
This property controls the addition of the -die switch, treat this property as a boolean.
- property error
Report errors.
This property controls the addition of the -error switch, treat this property as a boolean.
- property filter
Read standard input, write standard output.
This property controls the addition of the -filter switch, treat this property as a boolean.
- property help
Report command line options.
More information on associated and general qualifiers can be found with -help -verbose
This property controls the addition of the -help switch, treat this property as a boolean.
- property options
Prompt for standard and additional values.
If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.
This property controls the addition of the -options switch, treat this property as a boolean.
- property outfile
Output filename
This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.
- property rformat
Output report file format
This controls the addition of the -rformat parameter and its associated value. Set this property to the argument value required.
- property stdout
Write standard output.
This property controls the addition of the -stdout switch, treat this property as a boolean.
- property verbose
Report some/full command line options
This property controls the addition of the -verbose switch, treat this property as a boolean.
- property warning
Report warnings.
This property controls the addition of the -warning switch, treat this property as a boolean.
- property wordsize
Word size to use for comparisons (10 default)
This controls the addition of the -wordsize parameter and its associated value. Set this property to the argument value required.
- class Bio.Emboss.Applications.IepCommandline(cmd='iep', **kwargs)
Bases:
_EmbossCommandLine
Commandline for EMBOSS iep: calculated isoelectric point and charge.
Examples
>>> from Bio.Emboss.Applications import IepCommandline >>> iep_cline = IepCommandline(sequence="proteins.faa", ... outfile="proteins.txt") >>> print(iep_cline) iep -outfile=proteins.txt -sequence=proteins.faa
You would typically run the command line with iep_cline() or via the Python subprocess module, as described in the Biopython tutorial.
- __init__(cmd='iep', **kwargs)
Initialize the class.
- property amino
Number of N-termini
Integer 0 (default) or more.
This controls the addition of the -amino parameter and its associated value. Set this property to the argument value required.
- property auto
Turn off prompts.
Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.
This property controls the addition of the -auto switch, treat this property as a boolean.
- property carboxyl
Number of C-termini
Integer 0 (default) or more.
This controls the addition of the -carboxyl parameter and its associated value. Set this property to the argument value required.
- property debug
Write debug output to program.dbg.
This property controls the addition of the -debug switch, treat this property as a boolean.
- property die
Report dying program messages.
This property controls the addition of the -die switch, treat this property as a boolean.
- property disulphides
Number of disulphide bridges
Integer 0 (default) or more.
This controls the addition of the -disulphides parameter and its associated value. Set this property to the argument value required.
- property error
Report errors.
This property controls the addition of the -error switch, treat this property as a boolean.
- property filter
Read standard input, write standard output.
This property controls the addition of the -filter switch, treat this property as a boolean.
- property help
Report command line options.
More information on associated and general qualifiers can be found with -help -verbose
This property controls the addition of the -help switch, treat this property as a boolean.
- property lysinemodified
Number of modified lysines
Integer 0 (default) or more.
This controls the addition of the -lysinemodified parameter and its associated value. Set this property to the argument value required.
- property notermini
Exclude (True) or include (False) charge at N and C terminus.
This controls the addition of the -notermini parameter and its associated value. Set this property to the argument value required.
- property options
Prompt for standard and additional values.
If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.
This property controls the addition of the -options switch, treat this property as a boolean.
- property outfile
Output filename
This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.
- property sequence
Protein sequence(s) filename
This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.
- property stdout
Write standard output.
This property controls the addition of the -stdout switch, treat this property as a boolean.
- property verbose
Report some/full command line options
This property controls the addition of the -verbose switch, treat this property as a boolean.
- property warning
Report warnings.
This property controls the addition of the -warning switch, treat this property as a boolean.
- class Bio.Emboss.Applications.SeqretCommandline(cmd='seqret', **kwargs)
Bases:
_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__(cmd='seqret', **kwargs)
Initialize the class.
- property auto
Turn off prompts.
Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.
This property controls the addition of the -auto switch, treat this property as a boolean.
- property debug
Write debug output to program.dbg.
This property controls the addition of the -debug switch, treat this property as a boolean.
- property die
Report dying program messages.
This property controls the addition of the -die switch, treat this property as a boolean.
- property error
Report errors.
This property controls the addition of the -error switch, treat this property as a boolean.
- property filter
Read standard input, write standard output.
This property controls the addition of the -filter switch, treat this property as a boolean.
- property help
Report command line options.
More information on associated and general qualifiers can be found with -help -verbose
This property controls the addition of the -help switch, treat this property as a boolean.
- property options
Prompt for standard and additional values.
If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.
This property controls the addition of the -options switch, treat this property as a boolean.
- property osformat
Output sequence(s) format (e.g. fasta, genbank)
This controls the addition of the -osformat parameter and its associated value. Set this property to the argument value required.
- property outseq
Output sequence file.
This controls the addition of the -outseq parameter and its associated value. Set this property to the argument value required.
- property sequence
Input sequence(s) filename
This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.
- property sformat
Input sequence(s) format (e.g. fasta, genbank)
This controls the addition of the -sformat parameter and its associated value. Set this property to the argument value required.
- property stdout
Write standard output.
This property controls the addition of the -stdout switch, treat this property as a boolean.
- property verbose
Report some/full command line options
This property controls the addition of the -verbose switch, treat this property as a boolean.
- property warning
Report warnings.
This property controls the addition of the -warning switch, treat this property as a boolean.
- class Bio.Emboss.Applications.SeqmatchallCommandline(cmd='seqmatchall', **kwargs)
Bases:
_EmbossCommandLine
Commandline object for the seqmatchall program from EMBOSS.
e.g. >>> cline = SeqmatchallCommandline(sequence=”opuntia.fasta”, outfile=”opuntia.txt”) >>> cline.auto = True >>> cline.wordsize = 18 >>> cline.aformat = “pair” >>> print(cline) seqmatchall -auto -outfile=opuntia.txt -sequence=opuntia.fasta -wordsize=18 -aformat=pair
- __init__(cmd='seqmatchall', **kwargs)
Initialize the class.
- property aformat
Display output in a different specified output format
This controls the addition of the -aformat parameter and its associated value. Set this property to the argument value required.
- property auto
Turn off prompts.
Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.
This property controls the addition of the -auto switch, treat this property as a boolean.
- property debug
Write debug output to program.dbg.
This property controls the addition of the -debug switch, treat this property as a boolean.
- property die
Report dying program messages.
This property controls the addition of the -die switch, treat this property as a boolean.
- property error
Report errors.
This property controls the addition of the -error switch, treat this property as a boolean.
- property filter
Read standard input, write standard output.
This property controls the addition of the -filter switch, treat this property as a boolean.
- property help
Report command line options.
More information on associated and general qualifiers can be found with -help -verbose
This property controls the addition of the -help switch, treat this property as a boolean.
- property options
Prompt for standard and additional values.
If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.
This property controls the addition of the -options switch, treat this property as a boolean.
- property outfile
Output filename
This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.
- property sequence
Readable set of sequences
This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.
- property stdout
Write standard output.
This property controls the addition of the -stdout switch, treat this property as a boolean.
- property verbose
Report some/full command line options
This property controls the addition of the -verbose switch, treat this property as a boolean.
- property warning
Report warnings.
This property controls the addition of the -warning switch, treat this property as a boolean.
- property wordsize
Word size (Integer 2 or more, default 4)
This controls the addition of the -wordsize parameter and its associated value. Set this property to the argument value required.