[BioRuby] problem while handling large fasta files

[Naohisa GOTO]

Hi,

Please show which BioRuby version, Ruby version, OS,
architecture (type of CPU) you are using.

Is the Ruby and/or BioRuby version older?

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

On Thu, 4 Sep 2008 14:02:19 +0200 (CEST)
"K. Patil" <kpatil at science.uva.nl> wrote:

> Hi,
> 
> I am trying to do some simple processing on fasta files. It works file for
> small files (upto several MB). But as soon as I move to very large files
> (e.g. 2.2 GB) the program crashes. Any help/suggestions highly
> appreciated.
> 
> Best regards,
> Kaustubh Patil
> 
> I am pasting a very simple example below (the file is 2.2GB);
> 
> irb(main):021:0> fasta = Bio::FastaFormat.open("9606.2.fna")
> => #<Bio::FlatFile:0x2b2484e9c4a0
> @splitter=#<Bio::FlatFile::Splitter::Default:0x2b2484e9a420
> @stream=#<Bio::FlatFile::BufferedInputStream:0x2b2484e9c158
> @io=#<Bio::FlatFile::BufferedInputStream:0x2b2484e9c3b0
> @io=#<File:9606.2.fna>, @buffer="", @path="9606.2.fna">,
> @buffer=">9606.2.fna\ntaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaac\n",
> @path="9606.2.fna">, @header=nil, @delimiter="\n>", @delimiter_overrun=1>,
> @firsttime_flag=true,
> @stream=#<Bio::FlatFile::BufferedInputStream:0x2b2484e9c158
> @io=#<Bio::FlatFile::BufferedInputStream:0x2b2484e9c3b0
> @io=#<File:9606.2.fna>, @buffer="", @path="9606.2.fna">,
> @buffer=">9606.2.fna\ntaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaac\n",
> @path="9606.2.fna">, @skip_leader_mode=:firsttime, @raw=false,
> @dbclass=Bio::FastaFormat>
> irb(main):022:0> fasta.each do |seq|
> irb(main):023:1* print seq.data
> irb(main):024:1> end
> NoMethodError: private method `sub' called for nil:NilClass
>         from /usr/lib/ruby/1.8/bio/db/fasta.rb:156:in `initialize'
>         from /usr/lib/ruby/1.8/bio/io/flatfile.rb:579:in `new'
>         from /usr/lib/ruby/1.8/bio/io/flatfile.rb:579:in `next_entry'
>         from /usr/lib/ruby/1.8/bio/io/flatfile.rb:609:in `each'
>         from (irb):22
> 
> 
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby