[Bioperl-l] poblems with object's locations

[Marc Logghe]

Hi Sergiy,
don't worry, it is only a typo:
it is Bio::SeqIO, with a 'q' not with a 'g'
                 ~
cheers,
Marc

> -----Original Message-----
> From: Sergiy Ivakhno [mailto:ivahser at i.com.ua]
> Sent: Thursday, July 10, 2003 6:25 AM
> To: bioperl-l at portal.open-bio.org
> Subject: [Bioperl-l] poblems with object's locations
> 
> 
> Greetings
> 
> I was trying to run the program on BioPerl 1.2.1 which I've 
> installed today 
> 
> ( installation went well ) using modules Bio::Seq and 
> Bio::SeqIO but the Perl5.8 gives an error massage 
> Can't locate object method "new" via package "Bio::SegIO" 
> (perhaps you forgot to load "Bio::SegIO"?) at 1.pl line 5.
> 
> I tried to specify exact pass to library through lib pragma 
> but it doesn't work .
> 
> Maybe I missed something ,I'm only beginner.
> 
> Below I appended the code .Thank you in advance for you suggestions .
> 
> Sergiy.
> 
> 
> 
> use Bio::Seq;
> 
> use Bio::SeqIO;
> 
> use lib '/usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO';
> 
> use lib '/usr/lib/perl5/site_perl/5.8.0/Bio/Seq';
> 
> $seqin = Bio::SegIO->new( -format =>'EMBL',-file=>'record.EMBL');
> 
> $seqout = Bio::SeqIO->new( -format => 'Fasta', -file => '>output.fa');
> 
> while ( my $seqobj->next_seq()){
> 
> print "Seen sequence",$seqobj->display_id,"start of seq",
> 
> substr($seqobj->seq,1,10),"\n";
> 
> if ($seqobj->moltipe eq "dna") {
> 
> $rev=$seqobj->revcom();
> 
> $id = $seqobj->display_id();
> 
> $id="$id.rev";
> 
> $rev->display_id($id);
> 
> $seqout->write_seq($rev);
> 
> }
> 
> foreach $feat ($seqobj->top_SeqFeature()){
> 
> if ($feat->primary_tag eq 'exon')
> 
> { print STDOUT "Location",$feat->start,":",
> 
> $feat->end,"CFF[".feat->gff_string,"]\n";
> 
> }}
> 
> }
> 
>  
>