<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Hi Swaraj,<br>
<br>
Unfortunately, the 'software' column for tetraodon is not populated.<br>
<br>
If you want a more reliable way of finding repeats from
repeatmasker, I would recommend using the analysis logic name
($analysis->logic_name)<br>
That field is compulsory and any repeat mask based analysis will be
named 'repeatmask%'<br>
<br>
<br>
Hope that helps,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 20/02/2014 15:53, swaraj basu wrote:<br>
</div>
<blockquote
cite="mid:CAKNnbJS_=L+nE2JSQThKS=4cpo1qQKCwRX-zirVesBJwP6+TVg@mail.gmail.com"
type="cite">
<div dir="ltr">
<div>
<div>Dear All,<br>
<br>
</div>
I want to fetch coordinates of repeat elements identified by
the repeat masker program in multiple species (BED format). I
am using the following code to get the desirable results<br>
<br>
<i>my $slice = $slice_adaptor->fetch_by_region( $csn, $srn
); </i>#csn AND srn ARE PREDEFINED BY ME <i><br>
my @repeats = @{ $slice->get_all_RepeatFeatures() };<br>
foreach my $repeat (@repeats) {<br>
my $id = $repeat->display_id();<br>
my $start = $repeat->start();<br>
my $end = $repeat->end();<br>
my $strand = $repeat->strand();<br>
my $score = $repeat->score();<br>
my $name = $csn.$srn;<br>
my $analysis = $repeat->analysis();<br>
my $program = $analysis->program();<br>
next unless $program eq "RepeatMasker";<br>
print "$name\t$start\t$end\t$id\t$score\t$strand\n";<br>
}</i><br>
<br>
</div>
<div>My code is fetching me results for human, mouse, zebrafish,
cavefish but for <i>Tetraodon</i>, the
$analysis->program() scalar remains undefined. Hence I am
unable to extract the RepeatMasker predictions on the <i>Tetraodon
</i>genome. Can someone please help.<br>
<br>
</div>
<div>-Regards<br>
<br>
Swaraj Basu<br>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
</body>
</html>