Bioperl

[jsun529]

I have try to use the get_SeqFeatures with the following code, however the output looks like there are some errors, not sure how to fix that, any help? Thanks.

#!/usr/bin/perl

use Bio::Perl;
use Bio::SeqIO;
#use Bio::Graphics;
use Bio::SeqFeature::Generic;

my $seqio = Bio::SeqIO->new(-fh => \*STDIN, -format => 'genbank');
while (my $seq = $seqio->next_seq()) {
# $seq is-a Bio::FeatureHolderI, hence:
my @feas = $seq->get_SeqFeatures();
# each element is-a Bio::SeqFeatureI
foreach my $fea (@feas) {
# do something with the feature objects
print "$fea\n";
}


output

Bio::SeqFeature::Generic=HASH(0x9f1d1c)
Bio::SeqFeature::Generic=HASH(0x9f03dc)
Bio::SeqFeature::Generic=HASH(0x9f0460)
Bio::SeqFeature::Generic=HASH(0x9f25e0)
Bio::SeqFeature::Generic=HASH(0x9f583c)
Bio::SeqFeature::Generic=HASH(0x9f2790)
Bio::SeqFeature::Generic=HASH(0x9f24d8)
Bio::SeqFeature::Generic=HASH(0x9f6334)
Bio::SeqFeature::Generic=HASH(0x9f6610)
Bio::SeqFeature::Generic=HASH(0x9f5cd4)

[Zigster]

this is just how perl works and is not a bug nor specific to bioperl

you are attempting to print an object to the display

you need to use one of the methods provided by that object to return something that is human-readable (i.e. a string)

try using the display_name method

http://doc.bioperl.org/releases/bioperl-1.4/Bio/SeqFeature/Generic.html#POD21

[jsun529]

Thanks. Do any one knows how to pass the objects from get_SeqFeatures, e.g. CDS/EXONS positions to the Bio::Coordinate::GeneMapper function to get different coordinate value? The doc is not very helpful at all. Thanks a lot

[Zigster]

From the genemapper documentation it looks like you'll need two things:

# get a Bio::RangeI representing the start, end and strand of the CDS
# in chromosomal (or entry) coordinates
my $cds;

# get a Bio::Location::Split or an array of Bio::LocationI objects
# holding the start, end and strand of all the exons in chromosomal
# (or entry) coordinates

the latter can be gleaned from the SeqFeature using the Location method, though you might have to put them into an array

http://doc.bioperl.org/releases/bioperl-1.4/Bio/SeqFeature/Generic.html#POD21

There are pretty good BioPerl mailing lists out there but I suggest you learn more basics about using perl objects before posting questions to one of those.

[jsun529]

I know the functions, however the documentation is not very clear without a good working example. which site is a better bioperl mailing list?

[jsun529]

how to I get the value out of this objects

[Zigster]

look at the methods and find one that returns an integer or a string

have you read through Beginning Perl for Bioinformatics and Mastering Perl for Bioinformatics?

I understand your frustration but I would not suggest posting to the bp boards. First familiarize yourself well with perl and then read every post you can about coordinates.

http://www.nabble.com/forum/Search.jtp?query=coordinate&local=y&forum=13596&daterange=0&startdate=&enddate=

[jsun529]

Thanks, not have much time with it, would like quick help to move on, however thanks anyway.