README.md in parse_fasta-2.2.0 vs README.md in parse_fasta-2.3.0

- old
+ new

@@ -22,10 +22,12 @@ ## Overview ## Provides nice, programmatic access to fasta and fastq files. It's faster and more lightweight than BioRuby. And more fun! +It takes care of a lot of whacky edge cases like parsing multi-blob gzipped files, and being strict on formatting by default. + ## Documentation ## Checkout [parse_fasta docs](http://rubydoc.info/gems/parse_fasta) for the full api documentation. @@ -88,8 +90,16 @@ But of course, since it is a `#to_s` override...you don't even have to call it directly! ```ruby ParseFasta::SeqFile.open(ARGV[0]).each_record do |rec| + puts rec +end +``` + +Sometimes your fasta file might have record separators (`>`) withen the "sequence". For example, CD-HIT's `.clstr` files have headers within what would be the sequence part of the record. `ParseFasta` is really strict about formatting and will raise an error when trying to read these types of files. If you would like to parse them, use the `check_fasta_seq: false` flag like so: + +```ruby +ParseFasta::SeqFile.open(ARGV[0], check_fasta_seq: false).each_record do |rec| puts rec end ```