<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div style="RIGHT: auto">Hi everyone,</div>
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<div style="RIGHT: auto">I have locally installed the ensembl database and using the ensembl api v<VAR id=yui-ie-cursor></VAR>60. However, when I tried to retrieve information from a transcript, I get the following error message:</div>
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<div style="RIGHT: auto"> -------------------- EXCEPTION --------------------<BR>MSG: Could not find start or end exon in transcript_id=510612</div>
<div style="RIGHT: auto">STACK Bio::EnsEMBL::DBSQL::TranslationAdaptor::fetch_by_Transcript /home/GraceCheng/src/ensembl.60/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm:256<BR>STACK Bio::EnsEMBL::Transcript::translation /home/GraceCheng/src/ensembl.60/modules/Bio/EnsEMBL/Transcript.pm:621<BR>STACK Bio::EnsEMBL::Transcript::cdna_coding_start /home/GraceCheng/src/ensembl.60/modules/Bio/EnsEMBL/Transcript.pm:844<BR>STACK toplevel ensembl_transcript.pl:74<BR>Ensembl API version = 60<BR>---------------------------------------------------<BR></div>
<div style="RIGHT: auto">I have no idea what is going on, could anyone help? Below is my script:</div>
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<div style="RIGHT: auto">my $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(<BR> -dbname => $opt{dbname},<BR> -user => $opt{dbuser},<BR> -pass => $opt{dbpass},<BR> -host => $opt{dbhost},<BR> -port => $opt{dbport},<BR> );</div>
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<div style="RIGHT: auto">my $tr_adaptor = $dba->get_TranscriptAdaptor;<BR>my $tl_adaptor = $dba->get_TranslationAdaptor; </div>
<div style="RIGHT: auto">my $DIR = "/home/GraceCheng/perl_scripts/ensembl_api";</div>
<div style="RIGHT: auto">my $infile = "$DIR/transcriptID_uniq.txt";</div>
<div style="RIGHT: auto">my $outfile = "./transcript_info.out";</div>
<div style="RIGHT: auto">open (INFILE, "<$infile") || die ("Could not open infile $infile\n");<BR>open(OUT, "> $outfile") || die ("Could not open outfile $outfile\n");</div>
<div style="RIGHT: auto">while( my $in_line = <INFILE> ) {<BR> chomp ($in_line);<BR> next if ($.==1);<BR> my @inline = split (/\t/, $in_line);<BR> <BR> my $trID = $inline[1];<BR> my $genename = $inline[0];<BR> <BR> my $tr = $tr_adaptor->fetch_by_stable_id($trID);<BR> <BR> if ($tr) {<BR> my $trname = $tr->external_name();<BR> my $start = $tr->start();<BR> my $end = $tr->end();<BR> my $chr = $tr->slice->seq_region_name();<BR> my $cdna_coding_start = $tr->cdna_coding_start();<BR> my $cdna_coding_end = $tr->cdna_coding_end();<BR> <BR> print OUT "$in_line\t";<BR> print OUT "chr$chr\:$start-$end\t$trname\t$cdna_coding_start\t$cdna_coding_end\n";</div>
<div style="RIGHT: auto"> }<BR>}</div>
<div style="RIGHT: auto">close (INFILE);<BR>close (OUT);</div>
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<div style="RIGHT: auto">Many thanks!</div>
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<div style="RIGHT: auto">Grace</div></div></body></html>