HWcloud

See also the lecture

For both tasks, submit your source code and the result, when run on whole dataset (s3://idzbucket2). The code is expected to use the MRJob framework presented in the lecture.

Task A

Count the number of occurrences of each 4-mer in the provided data.

Task B

Count the number of pairs of reads which overlap in exactly 30 bases (end of one read overlaps beginning of the second read). You can ignore reverse complement.

Hints:

• Try counting pairs for each 30-mer first.
• You can yield something structured from Mapper (e.g. tuple).
• There is a two-step MapReduce, which can help you with the final summation: https://pythonhosted.org/mrjob/guides/writing-mrjobs.html