Fasta performance comparison

I wanted to add performance metrics for fasta format files since their simplicity means that they are often used to transmit large sequences; the main intended use case of the lazy loading parsers. Fasta files don't contain extensive annotations or any features so the primary task of parsing a fasta file is parsing the sequence. Included below are the compared times for both a large file and a medium sized file.

Here we can see that the lazy loader's sequence reading is about 20% slower for the full range. As with genbank files, lazy loading is much better when using slices to access only a portion of a record. Reading five percent of the sequence results in the expected 95% time savings when using the lazy loading parser. The results posted here and those in my previous blog post were made using Python 3.4.


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