R

Perl vs Python vs Ruby: Parsing Fasta Files

Parsing fasta files is the single most common thing one does when working with sequencing data, so any programming language used should do the parsing efficiently and succinctly. Unfortunately due to the history of the format and the length of time it has been in use it has some archaic features, line wrapping and (sometimes) limited header size for example. Many people from a biologist background who first try to parse fasta files see this as a header followed by lines, so simply read the file line by line, appending the sequence as they go, and checking for a new header as you read.

devtools

Tools to Make Developing R Packages Easier