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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;"><font size="2"><span style="font-size:10pt;">Hi,<br>
<br>
I'm having trouble retrieving start and end positions of clones within a contig, using project() in ensembl release 62.<br>
<br>
I have a relatively empty database (only meta, assembly, coord_system and seq_region tables are non-empty) which contains the details of an FPC generated physical map. The clones have defined start and end positions on their respective contigs, but no respective
sequence data. They are not truncated; the cmp_start and cmp_end values are always the beginning and end of the clone, and the asm_start/end positions of a clone are permitted to overlap those of other clones.<br>
<br>
When I project a contig back onto the 'clone' coordinate level, I receive a tiling path for that contig which is consistent with the asm_start values of each clone within the contig. However, if I try to retrieve the start position of any clone (to_Slice()->start()),
it returns the wrong value (always '1') and the end position is always the length of the clone in question. The values returned by from_start() and from_end() are also incorrect (although they are do at least increase with each clone in the path, and are consistent
with the length of a given clone).<br>
<br>
...<br>
my $fpcCtg = $sa->fetch_by_region('fpc_ctg',$current_ctg);<br>
foreach my $cloneProj (@{$fpcCtg->project('clone')}){<br>
my $clone = $cloneProj->to_Slice();<br>
print $fpcCtg->seq_region_name(), ':',<br>
$cloneProj->from_start(), '-',<br>
$cloneProj->from_end(), ' -> ',<br>
$clone->seq_region_name(), ':',<br>
$clone->start(), '-',$clone->end(), '-',<br>
$clone->strand(), "\n";<br>
}<br>
...<br>
Output:<br>
ctg6:1-97000 -> 3DL140_K09:1-97000-1<br>
ctg6:112001-208000 -> 3DL041_A17:1-96000-1<br>
ctg6:239001-331000 -> 3DL106_D16:1-92000-1<br>
ctg6:380001-536000 -> 3DL140_K10:1-156000-1<br>
ctg6:641001-731000 -> 3DL031_J17:1-90000-1<br>
...<br>
<br>
Is there any way to retrieve the values of asm_start/end using project()? Or should I directly retrieve this using a mysql query?<br>
<br>
Thanks,<br>
<br>
Martin Ayling</span></font></div>
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