Python Programming for Biology: Bioinformatics and Beyond

Using the HTSeq library

Now we come to actually using the result of a short-read to genome alignment to illustrate

how  the  results  may  be  analysed.  For  this  section  we  will  be  making  use  of  the  HTSeq

library,  which  is  not  a  standard  Python  module,  but  which  should  be  downloaded  and

installed  separately.

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 All  of  the  following  could  be  done  with  pure  Python  and  its

standard libraries, but by using this extra module we will be making the job much easier,

and  this  will  hopefully  result  in  the  ability  to  do  more  science.  Also,  we  could  consider

using  other  packages  like  Pysam,

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 which  can  read  genomic  alignments,  though  overall

HTSeq provides more diverse functionality.

To  use  the  HTSeq  library,  once  it  is  properly  installed,  we  simply  import  it  into  our

Python programs. The imports give the ability to read several bioinformatics file formats:

FASTQ  for  the  sequence  reads,  SAM  for  the  genome  alignment  results  and  GFF  files

which give the genome annotation information (e.g. where the genes lie in the sequence),

to  which  we  can  relate  the  high-throughput  sequencing  data.  The  GenomicArray  and

GenomicInterval  imports  are  object  classes  that  we  will  use  to  hold  the  sequence

information in an efficient and easily accessible manner. Next some imports are made to

make graphs with the matplotlib library and the usual NumPy module to handle numeric

arrays with which we can do the mathematics.

from HTSeq import FastqReader, SAM_Reader, GFF_Reader

from HTSeq import GenomicArray, GenomicInterval

from matplotlib import pyplot

from numpy import array