Re: Genome UV Mutation Script -- Critique

You should really take a look at Bioperl. It ships with a Genbank parser. Would be something like

my $seq_io = Bio::SeqIO->new( -file => $file, format => 'genbank');
my $whole_genome = $seq_io->next_seq;
[download]

See perldoc Bio::SeqIO.

This parser is quite robust...Which is important as you will notice when you screen many different species ;)

Comment on Re: Genome UV Mutation Script -- Critique Download Code

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Re^2: Genome UV Mutation Script -- Critique by BrowserUk (Patriarch) on Mar 15, 2007 at 04:54 UTC
Be aware. Bio::SeqIO may be robust, but unless thing have changed in the last 6 months, it is very, very (ludicrously) slow. Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error. "Science is about questioning the status quo. Questioning authority". In the absence of evidence, opinion is indistinguishable from prejudice. "Too many [] have been sedated by an oppressive environment of political correctness and risk aversion."	[reply]
Re^3: Genome UV Mutation Script -- Critique by lima1 (Curate) on Mar 15, 2007 at 09:20 UTC
thats not really an issue with this small prokaryotic genomes. Update: i was curious and tried this with Bioperl. It is indeed MUCH slower. Thanks for the hint.	[reply]