A stateful C function for R: parsing Fasta sequences

April 19, 2010

(This article was first published on YOKOFAKUN, and kindly contributed to R-bloggers)

In the following post, I’ll create a C extension for R. This extension will iterate over all the FASTA sequences in a file and will return a pair(name,sequence) for each sequence, that is to say that I won’t store all the sequences in memory.The C codeThe structure FastaHandler holds the state of the fasta parser. It contains a pointer to the FILE, the current sequence and fasta header. We also

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