Python Programming for Biology: Bioinformatics and Beyond

Python examples

For some of the Python examples relating to high-throughput sequence analysis we will be

using  the  HTSeq  library  (see

http://www.cambridge.org/pythonforbiology

 for  download

and installation instructions) and will not attempt to write our own classes of object. This

is a fast library providing objects that deal with genomes, sequences and annotations etc. It

is especially helpful in simplifying the reading and writing of the various data file formats

that are used to store sequence and sequence-related data. For example, we will use it to

load FASTQ

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files that contain the sequencing information that comes from a sequencing

machine  and  GFF

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 files  containing  genome  annotation  information.  Initially  we  will

illustrate how to obtain genome sequences and map sequence reads, albeit controlling an

external  program  to  index  the  genome  and  do  the  actual  Burrows-Wheeler  alignment.

Next  we  will  load  the  resulting  alignment  information  to  show  how  the  results  can  be

accessed  in  Python,  including  making  graphs.  Finally  we  illustrate  how  to  link  the

alignment results, and thus the DNA sequence reads, to genomic annotations that describe

genes, exons, introns and such like.

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