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Exercise 6 PDF

The document describes two Hadoop exercises: 1) a word count program that counts the frequency of words in texts from Shakespeare and the Bible, and 2) a k-mer counting program that counts overlapping k-length sequences in a genome file to find the most common k-mers. It provides instructions on running hadoop jar to perform word counting on sample input files and find the top 10 words, and on implementing k-mer counting to find the top 10 most frequent 9-mers in an E. coli genome file.

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287 views

Exercise 6 PDF

The document describes two Hadoop exercises: 1) a word count program that counts the frequency of words in texts from Shakespeare and the Bible, and 2) a k-mer counting program that counts overlapping k-length sequences in a genome file to find the most common k-mers. It provides instructions on running hadoop jar to perform word counting on sample input files and find the top 10 words, and on implementing k-mer counting to find the top 10 most frequent 9-mers in an E. coli genome file.

Uploaded by

việt lê
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© © All Rights Reserved
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Download as PDF, TXT or read online on Scribd
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Exercise 6

1. Hadoop Word Count


The next program to test is the hadoop word count program. This example reads text files and
counts how often words occur. The input is text files and the output is text files, each line of which
contains a word and the count of how often it occured, separated by a tab.
Each mapper takes a line as input and breaks it into words. It then emits a key/value pair of the
word and 1. Each reducer sums the counts for each word and emits a single key/value with the
word and sum. As an optimization, the reducer is also used as a combiner on the map outputs. This
reduces the amount of data sent across the network by combining each word into a single record.
Before you can run the example, you'll have to copy some data into the distributed filesystem
(HDFS). Here we will create an input directory, and copy in the complete works of Shakespeare
and the bible (a standard large corpus for text mining)
The datafile is also avalable at - make sure to gunzip after downloading: bible+shakes.nopunc.gz
$ hadoop fs -mkdir /user/USERNAME/wordcount

$ hadoop fs -mkdir /user/USERNAME/wordcount/input

$ hadoop fs -put /bluearc/data/schatz/data/textmining/bible+shakes.nopunc


/user/mschatz/wordcount/input

To run the example, the command syntax is


$ hadoop jar /usr/lib/hadoop/hadoop-examples.jar wordcount \

/user/USERNAME/wordcount/input \

/user/USERNAME/wordcount/output

After this completes, download the results to your local directory like this:
$ hadoop fs -get /user/USERNAME/wordcount/output output

Question: What are the top 10 most frequently used words in the corpus?
Hint: Use the unix commands sort and head to scan the output file

2. Hadoop Kmer Counting


The next exercise will be to implement a kmer counter using hadoop. Conceptually this is very
similar to the wordcount program, but since there are no spaces in the human genome, we will
count overlapping kmers instead of discrete words.
The idea is if the genome is:
>chr1

ACACACAGT
And we are counting 3-mers, your map function will output
ACA 1

CAC 1

ACA 1

CAC 1

ACA 1

CAG 1

AGT 1

The shuffle function will sort them so the same key comes right after each other
ACA 1

ACA 1

ACA 1

CAC 1

CAC 1

CAG 1

AGT 1

And your reducer will output:


ACA 3

CAC 2

CAG 1

AGT 1

You can implement this in Java, using the WordCount program as an example, or you can use
Hadoop Streaming to implement it in any language you would like.
The Hadoop Streaming documentation describes how to use it:
https://hadoop.apache.org/docs/r1.2.1/streaming.html
And here is a nice tutorial using Python:
http://www.michael-noll.com/tutorials/writing-an-hadoop-mapreduce-program-in-python/
The genome file is available here: ecoli.fa.gz
Question: What are the top 10 most frequently occurring 9-mers in E coli?

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