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lecture_notes:05-29-2015 [2015/05/29 18:30] chkan created |
lecture_notes:05-29-2015 [2015/05/29 18:37] (current) chkan Added figures |
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Basic Kmer Counting | Basic Kmer Counting | ||
- | - Naïve python way [insert picture] | + | - Naïve python way (See Figure 1) |
○ Okay if you're in a microbial genome | ○ Okay if you're in a microbial genome | ||
○ Runs out of memory | ○ Runs out of memory | ||
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○ Process Kmers one character at a time to avoid building big strings | ○ Process Kmers one character at a time to avoid building big strings | ||
§ Look at sequences a kmer at a time | § Look at sequences a kmer at a time | ||
- | ○ How to compress results | + | ○ How to compress results (See Figure 2) |
§ Strings are inefficient way to store kmers | § Strings are inefficient way to store kmers | ||
§ Want to compress keys and values | § Want to compress keys and values | ||
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</code> | </code> | ||
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+ | Figure 1 | ||
+ | {{:lecture_notes:lecture051915_fig1.jpg?400|}} | ||
+ | |||
+ | ---- | ||
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+ | Figure 2 | ||
+ | {{:lecture_notes:lecture051915_fig2.jpg?200|}} |