[Bioperl-l] poblems with object's locations

[Hilmar Lapp]

On Thursday, July 10, 2003, at 05:43  AM, Marc Logghe wrote:

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

And for use lib only specify the root of the tree:

>>
>> use lib '/usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO';
>>
>> use lib '/usr/lib/perl5/site_perl/5.8.0/Bio/Seq';

instead do

	use lib '/usr/lib/perl5/site_perl/5.8.0';

which suspiciously looks like your standard site-perl path, so you 
probably can leave that out completely as it's in perl's search path 
already.

	-hilmar

>>
>> $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";
>>
>> }}
>>
>> }
>>
>>
>>
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-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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