biostrings: handling genomic information as strings

The module reflects the content of the R/Bioconductor package Biostrings. It defines Python-level classes for the R/S4 classes, and gives otherwise access to R-level commands the usual rpy2:robjects way.

The variable biostrings_env in the module is an rpy2.robjects.REnvironment for the modules namespace. Accessing explicitly a module’s object is then straightforward. Example:

>>> biostrings.biostrings_env['RNA_ALPHABET']

The class inheritance diagram is useful for having an overview of how (biological) strings are modelled.

A module to model the Biostrings library in Bioconductor

Copyright 2009-2010 - Laurent Gautier

class bioc.biostrings.AAString(*args, **kwargs)

classmethod new(x)

Parameter:x – a string of amino-acids

class bioc.biostrings.AAStringSet

Set of amino-acid strings

classmethod new(x)

class bioc.biostrings.AlignedXStringSet

class bioc.biostrings.AlignedXStringSet0

alphabet

as_character()

end

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

get_alphabet()

indel()

nchar

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

start

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

unaligned

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

width

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

class bioc.biostrings.BString(*args, **kwargs)

Biological string

classmethod new(x)

Parameter:x – a (biological) string

class bioc.biostrings.BStringSet

Set of biological strings

classmethod new(x)

class bioc.biostrings.DNAString(*args, **kwargs)

DNA string

classmethod new(x)

Parameter:x – a DNA string

reverse_complement()

Return the reverse complement

class bioc.biostrings.DNAStringSet

Set of DNA strings

classmethod new(x)

class bioc.biostrings.InDel

deletion

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

insertion

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

class bioc.biostrings.MTB_PDict

class bioc.biostrings.MaskedAAString

Masked string of amino-acids

class bioc.biostrings.MaskedBString

Masked biological string

class bioc.biostrings.MaskedDNAString

Masked DNA string

class bioc.biostrings.MaskedRNAString

Masked RNA string

class bioc.biostrings.MaskedXString

“Masked” arbitrary string

get_masks()

get_unmasked()

Return the strings without its ‘mask’

masks

Property for both R’s ‘masks’ and ‘masks<-‘

set_masks(value)

unmasked

Return the strings without its ‘mask’

class bioc.biostrings.PDict

Dictionnary of probes, that is dictionary of of rather short strings.

count(subject, algorithm='auto', max_mismatch=0, fixed=True, verbose=False)

Count the number of matching subject sequences

classmethod create_instance(x)

Create a preprocessed dictionnary of genomic patterns.

Parameter:x – a string vector, and DNAStringSet, or an XStringViews with s DNAString subject

match(subject, algorithm='auto', max_mismatch=0, fixed=True, verbose=False)

Match subject sequence(s) to the dictionary

which(subject, algorithm='auto', max_mismatch=0, fixed=True, verbose=False)

width

class bioc.biostrings.PairwiseAlignedFixedSubject

class bioc.biostrings.PairwiseAlignedFixedSubjectSummary

class bioc.biostrings.PairwiseAlignedXStringSet

static fromCharacter_Character(pattern, target, **kwargs)

static fromCharacter_missing(pattern, **kwargs)

static fromXString_XString(pattern, target, **kwargs)

nchar

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

nindel

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

pattern

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

score

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

class bioc.biostrings.PhredQuality

classmethod new(x)

class bioc.biostrings.QualityScaledAAStringSet

classmethod new(x, quality)

class bioc.biostrings.QualityScaledBStringSet

classmethod new(x, quality)

class bioc.biostrings.QualityScaledDNAStringSet

classmethod new(x, quality)

class bioc.biostrings.QualityScaledRNAStringSet

classmethod new(x, quality)

class bioc.biostrings.QualityScaledXStringSet

class bioc.biostrings.RNAString(*args, **kwargs)

RNA string

classmethod new(x)

Parameter:x – an RNA string

reverse_complement()

Return the reverse complement

class bioc.biostrings.RNAStringSet

Set of RNA strings

classmethod new(x)

class bioc.biostrings.SolexaQuality

classmethod new(x)

class bioc.biostrings.TB_PDict

‘Trusted-band’ (TB) probe dictionary

get_tb()

get_tb_width()

tb

tb_width

class bioc.biostrings.XString(*args, **kwargs)

Arbitrary string

alphabet

get_alphabet()

nchar

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

reverse()

class bioc.biostrings.XStringQuality

class bioc.biostrings.XStringSet

An abstract class, parent to *StringSet classes

subset(x)

class bioc.biostrings.XStringViews

View on an arbitrary string

as_matrix(**kwargs)

get_nchar()

nchar

reverse_complement()

Return the reverse and complement for the view

width

bioc.biostrings.biostrings_conversion(robj)

bsgenome: strings information for a complete genome

Examples

>>> import bioc.bsgenome
>>> genomes = bioc.bsgenome.__rpackage__.available_genomes()
>>> tuple(genomes)
('BSgenome.Amellifera.BeeBase.assembly4',
 'BSgenome.Amellifera.UCSC.apiMel2',
 'BSgenome.Athaliana.TAIR.01222004',
 'BSgenome.Athaliana.TAIR.04232008',
 'BSgenome.Btaurus.UCSC.bosTau3',
 'BSgenome.Btaurus.UCSC.bosTau4',
 'BSgenome.Celegans.UCSC.ce2',
 'BSgenome.Cfamiliaris.UCSC.canFam2',
 'BSgenome.Dmelanogaster.UCSC.dm2',
 'BSgenome.Dmelanogaster.UCSC.dm3',
 'BSgenome.Drerio.UCSC.danRer5',
 'BSgenome.Ecoli.NCBI.20080805',
 'BSgenome.Ggallus.UCSC.galGal3',
 'BSgenome.Hsapiens.UCSC.hg17',
 'BSgenome.Hsapiens.UCSC.hg18',
 'BSgenome.Hsapiens.UCSC.hg19',
 'BSgenome.Mmusculus.UCSC.mm8',
 'BSgenome.Mmusculus.UCSC.mm9',
 'BSgenome.Ptroglodytes.UCSC.panTro2',
 'BSgenome.Rnorvegicus.UCSC.rn4',
 'BSgenome.Scerevisiae.UCSC.sacCer1',
 'BSgenome.Scerevisiae.UCSC.sacCer2')

The genome names can be passed to biocLite (see the introduction) for an automagic download and install of the corresponding genome package.

>>> tuple(bioc.bsgenome.__rpackage__.installed_genomes())
('BSgenome.Celegans.UCSC.ce2',
 'BSgenome.Hsapiens.UCSC.hg18',
 'BSgenome.Hsapiens.UCSC.hg19')

Installed genomes can be imported, since they are R packages.

>>> from rpy2.robjects.packages import importr
>>> ce2_genome = importr('BSgenome.Celegans.UCSC.ce2')

>>> ce2_genome.Celegans
<BSgenome - Python:0x2a80058 / R:0x4cbdf10>
>>> print(ce2_genome.Celegans.seqlengths)
    chrI    chrII   chrIII    chrIV     chrV     chrX     chrM
15080483 15279308 13783313 17493791 20922231 17718849    13794
>>> ce2_genome.Celegans['chrI']
<DNAString - Python:0x2a80878 / R:0x53ac7e4>

Docstrings

The class inheritance diagram is useful for having an overview of how the representation of genomes is organized.

A module to model the BSgenome library in Bioconductor

Copyright 2009 - Laurent Gautier

class bioc.bsgenome.BSgenome

Arbitrary string

mseqnames

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

seqlengths

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

seqnames

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

class bioc.bsgenome.GenomeData

organism

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

provider

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

provider_version

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

class bioc.bsgenome.GenomeDataList

class bioc.bsgenome.GenomeDescription

organism

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

provider

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

provider_version

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

release_date

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

release_name

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

species

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

bioc.bsgenome.bsgenome_conversion(robj)