Task 1

Write a FASTA parser

Your solution should:

• be a Java code of high quality (maintability, reusability, OO design, etc)
• be efficient
• be capable of reading badly formatted FASTA files
• be capable of reading large files
• has convenient API
• be possible to extend to reading FASTQ files

Please refrain from using any libraries that are not part of a standard Java 6 development kit in your production code. For testing code fill free to use any library you feel comfortable with.

Task 2

Write a FASTA writer

• Use your parser to read a FASTA file which contains sequences with ambiguous characters (you choose whether this is going to be ambiguous DNA or protein sequence)
• Write two FASTA output files one with sequences which contains ambiguous characters and another one without.

Submission

Please submit your completed exercise to gsocexercise at gmail dot com by Friday the 6 of April inclusive. Your submission should be a ZIP archive that contains an executable JAR file with your FASTA parser and writer as well as

• your source files in the src directory
• your documentation files in the docs directory
• the test data file named data.fasta up to 10Kb in size
• The executable JAR containing the program. This should be called runme.jar.
• a pure ASCII text file called choices.txt describing the significant design choices you made, uncertainties you had regarding the project, and the decisions you made when resolving them.