shortread: handle short reads

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

Examples

>>> import bioc.shortread as shortread
>>> from rpy2.robjects.packages import importr
>>> base = importr('base')

Get the path to a FASTAQ file bundled with the R package. This is a small file, convenient to use as an example

>>> fp = base.system_file('extdata', package='ShortRead')

Now reading the data can used by calling directly the bioconductor functions.

>>> sr_pack = shortread.__rpackage__
>>> spath = sr_pack.SolexaPath(fp)
>>> rfq = sr_pack.readFastq(sr_pack.analysisPath(spath), pattern = "s_1_sequence.txt")
>>> rfq
<ShortReadQ - Python:0xca8376c / R:0xcd01cf8>

The class ShortReadQ has methods (mirroring the S4 methods in the R packages), and can be used as if an usual Python class.

For example, looking at the width for the first 10 reads:

>>>  tuple(rfq.width[1:10])
(36, 36, 36, 36, 36, 36, 36, 36, 36)

Now on to reading aligned reads:

>>> aln = shortread.__rpackage__.readAligned(spath, "s_2_export.txt")
>>> aln
<AlignedRead - Python:0xce66a0c / R:0xd0c7f98>

Note

The function shortread.__rpackage__.readALined() can be specified the source of alignment data.

• bowtie: type = “Bowtie”
• MAQ: type=”MAQMapShort”, or type=”MAQMap”, or type=”MAQMapview”

Reads can be accessed:

>>> aln.do_slot('sread')
<DNAStringSet - Python:0xce7a0ac / R:0xd0c9484>

Note

In bioconductor, sread() is not formally declared as method of class AlignedRead, so we access it as a slot.

Filters can be used to extract subsets of the reads:

>>> # chromosome 5
>>> chromfilter = shortread.__rpackage__.chromosomeFilter('chr5.fa')
>>> aln_chr5 = aln.rx(chromfilter(aln))
>>> # position interval 6E6-10E6
>>> posfilter = shortread.__rpackage__.positionFilter(min=6E6, max=10E6)
>>> print(aln_chr5.rx(posfilter(aln_chr_5)))
class: AlignedRead
length: 1 reads; width: 35 cycles
chromosome: 1
position: 6774915
strand: 1
alignQuality: NumericQuality
alignData varLabels: run lane ... filtering contig

Docstrings

The class inheritance diagram presents the parent-child relationships between the elements.

A module to model the ShortRead library in Bioconductor

Copyright 2009 - Laurent Gautier

class bioc.shortread.AlignedDataFrame

append(**kwargs)

class bioc.shortread.AlignedRead

coverage(start=NA, end=NA, coords=<StrVector - Python:0x59926e8 / R:0x909df08>, extend=0)

rx(i, drop=True)

class bioc.shortread.ArrayIntensity

class bioc.shortread.ExperimentPath

detail()

class bioc.shortread.FastqQuality

alphabetbycycle()

alphabetfrequency()

srduplicated()

srorder()

srrank()

class bioc.shortread.IntegerQuality

class bioc.shortread.Intensity

class bioc.shortread.IntensityInfo

class bioc.shortread.IntensityMeasure

class bioc.shortread.MatrixQuality

class bioc.shortread.NumericQuality

class bioc.shortread.QualityScore

detail()

width

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

class bioc.shortread.RochePath

detail()

read454()

readfasta(**kwargs)

readpath()

readqual(**kwargs)

rocheset()

runnames()

class bioc.shortread.RocheSet

class bioc.shortread.SFastqQuality

class bioc.shortread.SRSet

class bioc.shortread.ShortRead

alphabetbycycle()

clean()

detail()

narrow(start=None, end=None, width=None, use_names=True)

srduplicated()

srorder()

srrank()

srsort()

tables(n=50)

width

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

class bioc.shortread.ShortReadQ

class bioc.shortread.SolexaIntensity

class bioc.shortread.SolexaIntensityInfo

class bioc.shortread.SolexaPath

detail()

readaligned(**kwargs)

readfastq(**kwargs)

readintensities(**kwargs)

readprb(**kwargs)

readqseq(**kwargs)

solexaset()

class bioc.shortread.SolexaSet

bioc.shortread.shortread_conversion(robj)