<div dir="ltr"><div>I also want to bring to notice another issue with the annotation of repeats in<i> Tetraodon </i>genome (API 74). Fetching the repeat name, class and type using the following code<br><i><br></i><i><br>my @repeats = @{ $slice->get_all_RepeatFeatures() };<br>
foreach my $repeat (@repeats) {</i><br><i> my $consensus = $repeat->repeat_consensus();<br> my $repeat_name = $consensus->name();<br> my $repeat_class = $consensus->repeat_class();<br> my $repeat_type = $consensus->repeat_type();</i><br>
<i>}</i><br><br><br></div><div>I found that the class and type are not defined for <i>Tetraodon. </i>For example<br><br><b>Organism Name Class Type</b><br></div><div><i><br>Tetraodon </i> TNDIRS1 Tet_repeat Tetraodon repeats<i><br>
<br></i></div><div>Fugu<i> </i>DrDIRS1 LTR/DIRS1 LTRs<i><br><br></i></div><div>Thus if I have to classify repeat families in <i>Tetraodon </i>I cannot directly use the information fetched from Ensembl, while for Fugu I can do the same.<br>
<br></div><div>-Regards<br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Feb 20, 2014 at 5:58 PM, swaraj basu <span dir="ltr"><<a href="mailto:projectbasu@gmail.com" target="_blank">projectbasu@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Thanks for the useful information.<br></div><div class="gmail_extra"><div><div class="h5"><br><br><div class="gmail_quote">
On Thu, Feb 20, 2014 at 5:13 PM, mag <span dir="ltr"><<a href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@ebi.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Hi Swaraj,<br>
<br>
Unfortunately, the 'software' column for tetraodon is not populated.<br>
<br>
If you want a more reliable way of finding repeats from
repeatmasker, I would recommend using the analysis logic name
($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<div><div><br>
<br>
<div>On 20/02/2014 15:53, swaraj basu wrote:<br>
</div>
</div></div><blockquote type="cite"><div><div>
<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></fieldset>
<br>
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</blockquote>
<br>
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<br></blockquote></div><br><br clear="all"><br></div></div><span class="HOEnZb"><font color="#888888">-- <br>Swaraj Basu<br>PhD Student (Bioinformatics - Functional Genomics)<br>Animal Physiology and Evolution<br>Stazione Zoologica Anton Dohrn<br>
Naples<br>
</font></span></div>
</blockquote></div><br><br clear="all"><br>-- <br>Swaraj Basu<br>PhD Student (Bioinformatics - Functional Genomics)<br>Animal Physiology and Evolution<br>Stazione Zoologica Anton Dohrn<br>Naples<br>
</div>