Commit dc0d9035 authored by Toby Hodges's avatar Toby Hodges
Browse files

expanded structure of README

parent 7053b0ff
......@@ -7,25 +7,51 @@ statistics about DNA sequences described in a [FASTA file*](#fasta-format).
Download or `git clone` this repository and then follow the instructions below.
#### Your Tasks
## The Exercise
#### Introduction
__Before__ you look at the sequence files in this repository, open the script in
your favourite editor and discuss ways in which it could be improved. Things to
think about might include
1. __Before__ you look at the sequence files in this repository, open the script in your favourite editor and discuss ways in which it could be improved. Things to think about might include
- How easy is it to understand what the script does?
- How robust is the script?
- Does it follow good coding standards?
- Does it do what it is supposed to?
- What problems can you foresee, if the script were to be shared with others or applied to a different sequence file?
2. Now run the script on `exampleSequences1.fasta`
- What problems can you foresee, if the script were to be shared with others or
applied to a different sequence file?
#### First Application
Now run the script on `exampleSequences1.fasta`
- Has this made you notice any more improvements that could be made?
3. What about if you run the script on `exampleSequences2.fasta`?
4. Make a copy of the script (or start from scratch if you prefer!) and make as many improvements to the code as you think are necessary to make it
- robust
- portable
- shareable
- easy to maintain/adapt
- do what it is supposed to do!
(__Note:__ You may be aware that the Biopython library includes functions and object classes to work with sequence objects. Please avoid using the library for these exercises.)
5. If you have time, try to further adapt the script to expand its functionality such that, given a file of protein sequences instead, it will produce counts of the different amino acids.
#### Exposure to The Real World
What about if you run the script on `exampleSequences2.fasta`? Does this help you
to notice any additional improvements that could be made?
#### Improving the Script
Make a copy of the script (or start from scratch if you prefer!) and make as
many improvements to the code as you think are necessary to make it
- robust
- portable
- shareable
- easy to maintain/adapt
- do what it is supposed to do!
(__Note:__ You may be aware that the Biopython library includes functions and
object classes to work with sequence objects. Please avoid using the library for
this exercise.)
#### Adapting the Script
If you have time, try to further adapt the script to expand its functionality
such that, given a file of protein sequences instead, it will produce counts of
the different amino acids.
#### *FASTA Format
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