[Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ?
Mark A. Jensen
maj at fortinbras.us
Mon Jan 19 17:03:31 EST 2009
Lincoln- that's great- thanks- MAJ
----- Original Message -----
From: Lincoln Stein
To: Mark A. Jensen
Cc: Dan Bolser ; bioperl-l at lists.open-bio.org
Sent: Monday, January 19, 2009 4:21 PM
Subject: Re: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ?
Hi Mark,
I've forwarded your bug report to the script's author.
Lincoln
On Mon, Jan 19, 2009 at 10:04 AM, Mark A. Jensen <maj at fortinbras.us> wrote:
Well, Dan,
You may get exactly what you need from the line of code you have written. Excellent!
However, genbank files can be complex, and will contain information that users may
want to manipulate in different ways, particularly in ways that are computable.
This script has other features under the hood, that you may not require, but at least
one person (the script's author) did.
One way to discover 'extra benefits' is to examine the script documentation, which
describes in detail the capabilities of the script. To access it, open the script file,
or use another possibly superfluous script that parses files in a particular context,
called "perldoc", like this:
perldoc genbank2gff3.PLS
It's also worth keeping in mind that BioPerl, as heavily object-oriented as it is, is
written to optimize development time, maybe at the expense of CPU cycles or
disk space. I have written my own modules that BioPerl could certainly have done,
but only with a generality that would have been pointless overhead for my application.
I can have a look at the error.
Best,
Mark
----- Original Message ----- From: "Dan Bolser" <dan.bolser at gmail.com>
To: <bioperl-l at lists.open-bio.org>
Sent: Monday, January 19, 2009 9:44 AM
Subject: [Bioperl-l] bp_genbank2gff3.pl vs. EMBL2GFF ?
I found the script 'bp_genbank2gff3.pl' gave an error and died while
trying to convert a .emb into GFF format.
head ~/perl5/bin/bp_genbank2gff3.pl
...
#$Id: genbank2gff3.PLS 15088 2008-12-04 02:49:09Z bosborne $;
bp_genbank2gff3.pl --format embl my.emb
Can't call method "binomial" on an undefined value at
~/perl5/bin/bp_genbank2gff3.pl line 690, <FH> line 347337.
However, looking at the docs, I came up with this:
perl -MBio::SeqIO -e '
$s = Bio::SeqIO->new( -file => shift )->next_seq;
print "# ", $s->feature_count, "\n";
print $_->gff_string, "\n" foreach $s->get_SeqFeatures
' my.emb > my.emb.gff
How come the BioPerl script is >1000 lines, and apparently the
conversion only requires 1? What extra benefit would I get from using
bp_genbank2gff3.pl (assuming it ran)?
Thanks for any feedback,
Dan.
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Lincoln D. Stein
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
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