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ComparaTutorial - Revision history
2024-03-28T18:48:27Z
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Cgrove at 18:18, 11 August 2010
2010-08-11T18:18:43Z
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 18:18, 11 August 2010</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> [http://www.perldoc.com/perl5.6/pod/func/print.html <span><font color="#000066">print</font></span>] <span><font color="#ff0000">"<span>'''<font color="#000099">\n</font>'''</span>"</font></span><nowiki>;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> [http://www.perldoc.com/perl5.6/pod/func/print.html <span><font color="#000066">print</font></span>] <span><font color="#ff0000">"<span>'''<font color="#000099">\n</font>'''</span>"</font></span><nowiki>;</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </nowiki><span><font color="#66cc66">}</font></span></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </nowiki><span><font color="#66cc66">}</font></span></div></td></tr>
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Cgrove
https://wiki.wormbase.org/index.php?title=ComparaTutorial&diff=15&oldid=prev
Tharris: New page: =Places= [ftp://ftp.sanger.ac.uk/pub2/wormbase/data/compara.tar.bz2 Compara tarball for WS163] (mysql dumps) [http://www.ensembl.org/info/software/compara/index.html Compara Page] (includ...
2007-09-23T19:09:36Z
<p>New page: =Places= [ftp://ftp.sanger.ac.uk/pub2/wormbase/data/compara.tar.bz2 Compara tarball for WS163] (mysql dumps) [http://www.ensembl.org/info/software/compara/index.html Compara Page] (includ...</p>
<p><b>New page</b></p><div>=Places=<br />
[ftp://ftp.sanger.ac.uk/pub2/wormbase/data/compara.tar.bz2 Compara tarball for WS163] (mysql dumps)<br />
<br />
[http://www.ensembl.org/info/software/compara/index.html Compara Page] (including how to install / API documentation)<br />
<br />
=EnsEMBL Registry=<br />
As the default GenomeDB locations in the database point to the Sanger setup, you should use a EnsEMBL registry to access yours.<br />
<br />
<br />
<span>''<font color="#808080"><nowiki># ensembl.reg</nowiki></font>''</span><br />
<span>'''<font color="#000000">use</font>'''</span> Bio::<span><font color="#006600">EnsEMBL</font></span><nowiki>::</nowiki><span><font color="#006600">Utils</font></span><nowiki>::</nowiki><span><font color="#006600">ConfigRegistry</font></span><nowiki>;<br />
</nowiki><span>'''<font color="#000000">use</font>'''</span> Bio::<span><font color="#006600">EnsEMBL</font></span><nowiki>::</nowiki><span><font color="#006600">DBSQL</font></span><nowiki>::</nowiki><span><font color="#006600">DBAdaptor</font></span><nowiki>;<br />
</nowiki><span>'''<font color="#000000">use</font>'''</span> Bio::<span><font color="#006600">EnsEMBL</font></span><nowiki>::</nowiki><span><font color="#006600">Compara</font></span><nowiki>::</nowiki><span><font color="#006600">DBSQL</font></span><nowiki>::</nowiki><span><font color="#006600">DBAdaptor</font></span><nowiki>;<br />
<br />
</nowiki><span>'''<font color="#000000">new</font>'''</span> Bio::<span><font color="#006600">EnsEMBL</font></span><nowiki>::</nowiki><span><font color="#006600">DBSQL</font></span><nowiki>::</nowiki><span><font color="#006600">DBAdaptor</font></span><span><font color="#66cc66">(</font></span>-host =&gt; <span><font color="#ff0000">'ia64b'</font></span>,-user=&gt;<span><font color="#ff0000">'wormro'</font></span>,-port=&gt; <span><font color="#cc66cc">3306</font></span>,<br />
-species =&gt; <span><font color="#ff0000">'Caenorhabditis elegans'</font></span>,-group =&gt; <span><font color="#ff0000">'core'</font></span>,-dbname =&gt; <span><font color="#ff0000">'worm_WB160'</font></span><span><font color="#66cc66">)</font></span><nowiki>;<br />
</nowiki><span>'''<font color="#000000">new</font>'''</span> Bio::<span><font color="#006600">EnsEMBL</font></span><nowiki>::</nowiki><span><font color="#006600">DBSQL</font></span><nowiki>::</nowiki><span><font color="#006600">DBAdaptor</font></span><span><font color="#66cc66">(</font></span>-host =&gt; <span><font color="#ff0000">'ia64b'</font></span>,-user=&gt;<span><font color="#ff0000">'wormro'</font></span>,-port=&gt; <span><font color="#cc66cc">3306</font></span>,<br />
-species =&gt; <span><font color="#ff0000">'Caenorhabditis briggsae'</font></span>,-group =&gt; <span><font color="#ff0000">'core'</font></span>,-dbname =&gt; <span><font color="#ff0000">'worm_ensembl_briggsae'</font></span><span><font color="#66cc66">)</font></span><nowiki>;<br />
</nowiki><span>'''<font color="#000000">new</font>'''</span> Bio::<span><font color="#006600">EnsEMBL</font></span><nowiki>::</nowiki><span><font color="#006600">DBSQL</font></span><nowiki>::</nowiki><span><font color="#006600">DBAdaptor</font></span><span><font color="#66cc66">(</font></span>-host =&gt; <span><font color="#ff0000">'ia64b'</font></span>,-user=&gt;<span><font color="#ff0000">'wormro'</font></span>,-port=&gt; <span><font color="#cc66cc">3306</font></span>,<br />
-species =&gt; <span><font color="#ff0000">'Caenorhabditis remanei'</font></span>,-group =&gt; <span><font color="#ff0000">'core'</font></span>,-dbname =&gt; <span><font color="#ff0000">'worm_ensembl_remanei'</font></span><span><font color="#66cc66">)</font></span><nowiki>;<br />
<br />
</nowiki><span>'''<font color="#000000">new</font>'''</span> Bio::<span><font color="#006600">EnsEMBL</font></span><nowiki>::</nowiki><span><font color="#006600">Compara</font></span><nowiki>::</nowiki><span><font color="#006600">DBSQL</font></span><nowiki>::</nowiki><span><font color="#006600">DBAdaptor</font></span><span><font color="#66cc66">(</font></span>-host =&gt; <span><font color="#ff0000">'ia64b'</font></span>,-user=&gt;<span><font color="#ff0000">'wormro'</font></span>,-port=&gt; <span><font color="#cc66cc">3306</font></span>,<br />
-species =&gt; <span><font color="#ff0000">'Compara'</font></span>,-dbname =&gt; <span><font color="#ff0000">'worm_compara_lagan'</font></span><span><font color="#66cc66">)</font></span><nowiki>;<br />
<br />
</nowiki><span><font color="#cc66cc">1</font></span><nowiki>;</nowiki><br />
<br />
Please replace whatever host/port/username/passowrd you use.<br />
<br />
It is a good idea to setup an environment variable to point at it: <code> setenv ENSEMBL_REGISTRY &lt;/path_to_registry/ensembl.reg&gt; </code><br />
<br />
= Genomic Alignments =<br />
<br />
<span>''<font color="#808080"><nowiki># 2-way.pl</nowiki></font>''</span><br />
<br />
<span>'''<font color="#000000">use</font>'''</span> strict;<br />
<span>'''<font color="#000000">use</font>'''</span> Bio::<span><font color="#006600">EnsEMBL</font></span><nowiki>::</nowiki><span><font color="#006600">Registry</font></span><nowiki>;<br />
</nowiki><span>'''<font color="#000000">use</font>'''</span> Bio::<span><font color="#006600">SimpleAlign</font></span><nowiki>;<br />
</nowiki><span>'''<font color="#000000">use</font>'''</span> Bio::<span><font color="#006600">AlignIO</font></span><nowiki>;<br />
</nowiki><span>'''<font color="#000000">use</font>'''</span> Bio::<span><font color="#006600">LocatableSeq</font></span><nowiki>;<br />
Bio::</nowiki><span><font color="#006600">EnsEMBL</font></span><nowiki>::</nowiki><span><font color="#006600">Registry</font></span>-&gt;<span><font color="#006600">load_all</font></span><span><font color="#66cc66">(</font></span><span><font color="#66cc66">)</font></span><nowiki>;<br />
<br />
</nowiki><span>''<font color="#808080"><nowiki># adaptors setup</nowiki></font>''</span><br />
<span><font color="#b1b100">my</font></span> <span><font color="#0000ff">$mlss_a</font></span> = Bio::<span><font color="#006600">EnsEMBL</font></span><nowiki>::</nowiki><span><font color="#006600">Registry</font></span>-&gt;<span><font color="#006600">get_adaptor</font></span><span><font color="#66cc66">(</font></span> <span><font color="#ff0000">'Compara'</font></span>, <span><font color="#ff0000">'compara'</font></span>, <span><font color="#ff0000">'MethodLinkSpeciesSet'</font></span> <span><font color="#66cc66">)</font></span><nowiki>;<br />
</nowiki><span><font color="#b1b100">my</font></span> <span><font color="#0000ff">$gdb_a</font></span> = Bio::<span><font color="#006600">EnsEMBL</font></span><nowiki>::</nowiki><span><font color="#006600">Registry</font></span>-&gt;<span><font color="#006600">get_adaptor</font></span><span><font color="#66cc66">(</font></span> <span><font color="#ff0000">'Compara'</font></span>, <span><font color="#ff0000">'compara'</font></span>, <span><font color="#ff0000">'GenomeDB'</font></span> <span><font color="#66cc66">)</font></span><nowiki>;<br />
</nowiki><span><font color="#b1b100">my</font></span> <span><font color="#0000ff">$ga_a</font></span> = Bio::<span><font color="#006600">EnsEMBL</font></span><nowiki>::</nowiki><span><font color="#006600">Registry</font></span>-&gt;<span><font color="#006600">get_adaptor</font></span><span><font color="#66cc66">(</font></span> <span><font color="#ff0000">'Compara'</font></span>, <span><font color="#ff0000">'compara'</font></span>, <span><font color="#ff0000">'GenomicAlignBlock'</font></span> <span><font color="#66cc66">)</font></span><nowiki>;<br />
</nowiki><span><font color="#b1b100">my</font></span> <span><font color="#0000ff">$dnaf_a</font></span> = Bio::<span><font color="#006600">EnsEMBL</font></span><nowiki>::</nowiki><span><font color="#006600">Registry</font></span>-&gt;<span><font color="#006600">get_adaptor</font></span><span><font color="#66cc66">(</font></span> <span><font color="#ff0000">'Compara'</font></span>, <span><font color="#ff0000">'compara'</font></span>, <span><font color="#ff0000">'DnaFrag'</font></span> <span><font color="#66cc66">)</font></span><nowiki>;<br />
<br />
</nowiki><span>''<font color="#808080"><nowiki># genome databases setup</nowiki></font>''</span><br />
<span><font color="#b1b100">my</font></span> <span><font color="#0000ff">$edb</font></span> = <span><font color="#0000ff">$gdb_a</font></span>-&gt;<span><font color="#006600">fetch_by_name_assembly</font></span><span><font color="#66cc66">(</font></span><span><font color="#ff0000">'Caenorhabditis elegans'</font></span><span><font color="#66cc66">)</font></span><nowiki>;<br />
</nowiki><span><font color="#b1b100">my</font></span> <span><font color="#0000ff">$bdb</font></span> = <span><font color="#0000ff">$gdb_a</font></span>-&gt;<span><font color="#006600">fetch_by_name_assembly</font></span><span><font color="#66cc66">(</font></span><span><font color="#ff0000">'Caenorhabditis briggsae'</font></span><span><font color="#66cc66">)</font></span><nowiki>;<br />
</nowiki><span><font color="#b1b100">my</font></span> <span><font color="#0000ff">$rdb</font></span> = <span><font color="#0000ff">$gdb_a</font></span>-&gt;<span><font color="#006600">fetch_by_name_assembly</font></span><span><font color="#66cc66">(</font></span><span><font color="#ff0000">'Caenorhabditis remanei'</font></span><span><font color="#66cc66">)</font></span><nowiki>;<br />
<br />
</nowiki><span><font color="#b1b100">my</font></span> <span><font color="#0000ff">$mlss</font></span> = <span><font color="#0000ff">$mlss_a</font></span>-&gt;<span><font color="#006600">fetch_by_method_link_type_GenomeDBs</font></span><span><font color="#66cc66">(</font></span> <span><font color="#ff0000">'MLAGAN'</font></span>, <span><font color="#66cc66">[</font></span> <span><font color="#0000ff">$edb</font></span>, <span><font color="#0000ff">$bdb</font></span>, <span><font color="#0000ff">$rdb</font></span> <span><font color="#66cc66">]</font></span> <span><font color="#66cc66">)</font></span><nowiki>;<br />
<br />
</nowiki><span><font color="#b1b100">my</font></span> <span><font color="#0000ff">$alignIO</font></span> = Bio::<span><font color="#006600">AlignIO</font></span>-&gt;<span><font color="#006600">newFh</font></span><span><font color="#66cc66">(</font></span><br />
-interleaved =&gt; <span><font color="#cc66cc">0</font></span>,<br />
-fh =&gt; \*<span>'''<font color="#000000">STDOUT</font>'''</span>,<br />
-[http://www.perldoc.com/perl5.6/pod/func/format.html <span><font color="#000066">format</font></span>] =&gt; <span><font color="#ff0000">'clustalw'</font></span>,<br />
-idlength =&gt; <span><font color="#cc66cc">10</font></span><br />
<span><font color="#66cc66">)</font></span><nowiki>;<br />
</nowiki><span><font color="#b1b100">my</font></span> <span><font color="#0000ff">@all_aligns</font></span><nowiki>;<br />
<br />
</nowiki><span>''<font color="#808080"><nowiki># get a DNA fragment</nowiki></font>''</span><br />
<span><font color="#b1b100">my</font></span> <span><font color="#0000ff">$dna_frag</font></span> = <span><font color="#0000ff">$dnaf_a</font></span>-&gt;<span><font color="#006600">fetch_by_GenomeDB_and_name</font></span><span><font color="#66cc66">(</font></span> <span><font color="#0000ff">$edb</font></span>, <span><font color="#ff0000">'CHROMOSOME_I'</font></span> <span><font color="#66cc66">)</font></span><nowiki>;<br />
<br />
</nowiki><span><font color="#b1b100">my</font></span> <span><font color="#0000ff">$all_blocks</font></span> = <span><font color="#0000ff">$ga_a</font></span>-&gt;<span><font color="#006600">fetch_all_by_MethodLinkSpeciesSet_DnaFrag</font></span><span><font color="#66cc66">(</font></span> <span><font color="#0000ff">$mlss</font></span>, <span><font color="#0000ff">$dna_frag</font></span>, <span><font color="#cc66cc">2000001</font></span>, <span><font color="#cc66cc">300000</font></span> <span><font color="#66cc66">)</font></span><nowiki>;<br />
<br />
</nowiki><span>''<font color="#808080"><nowiki># for all aligned blocks</nowiki></font>''</span><br />
<span><font color="#b1b100">foreach</font></span> <span><font color="#b1b100">my</font></span> <span><font color="#0000ff">$align</font></span> <span><font color="#66cc66">(</font></span>@<span><font color="#0000ff">$all_blocks</font></span><span><font color="#66cc66">)</font></span> <span><font color="#66cc66">{</font></span><br />
<span><font color="#b1b100">my</font></span> <span><font color="#0000ff">$simple_align</font></span><nowiki>=</nowiki><span><font color="#0000ff">$align</font></span>-&gt;<span><font color="#006600">get_SimpleAlign</font></span><nowiki>;<br />
</nowiki>[http://www.perldoc.com/perl5.6/pod/func/push.html <span><font color="#000066">push</font></span>]<span><font color="#66cc66">(</font></span><span><font color="#0000ff">@all_aligns</font></span>,<span><font color="#0000ff">$simple_align</font></span><span><font color="#66cc66">)</font></span><nowiki>;<br />
</nowiki><span><font color="#66cc66">}</font></span><br />
<br />
<span><font color="#b1b100">foreach</font></span> <span><font color="#b1b100">my</font></span> <span><font color="#0000ff">$aln</font></span><span><font color="#66cc66">(</font></span><span><font color="#0000ff">@all_aligns</font></span><span><font color="#66cc66">)</font></span><span><font color="#66cc66">{</font></span><br />
[http://www.perldoc.com/perl5.6/pod/func/print.html <span><font color="#000066">print</font></span>] <span><font color="#0000ff">$alignIO</font></span> <span><font color="#0000ff">$aln</font></span><nowiki>;<br />
</nowiki><span><font color="#66cc66">}</font></span><br />
<br />
= Syntenic Regions =<br />
<br />
<span>''<font color="#808080"><nowiki># syntenic_regions.pl</nowiki></font>''</span><br />
<br />
<span>'''<font color="#000000">use</font>'''</span> strict;<br />
<span>'''<font color="#000000">use</font>'''</span> Bio::<span><font color="#006600">EnsEMBL</font></span><nowiki>::</nowiki><span><font color="#006600">Registry</font></span><nowiki>;<br />
Bio::</nowiki><span><font color="#006600">EnsEMBL</font></span><nowiki>::</nowiki><span><font color="#006600">Registry</font></span>-&gt;<span><font color="#006600">load_all</font></span><span><font color="#66cc66">(</font></span><span><font color="#66cc66">)</font></span><nowiki>;<br />
<br />
</nowiki><span><font color="#b1b100">my</font></span> <span><font color="#0000ff">$mlssa</font></span> = Bio::<span><font color="#006600">EnsEMBL</font></span><nowiki>::</nowiki><span><font color="#006600">Registry</font></span>-&gt;<span><font color="#006600">get_adaptor</font></span><span><font color="#66cc66">(</font></span> <span><font color="#ff0000">'Compara'</font></span>, <span><font color="#ff0000">'compara'</font></span>, <span><font color="#ff0000">'MethodLinkSpeciesSet'</font></span> <span><font color="#66cc66">)</font></span><nowiki>;<br />
</nowiki><span><font color="#b1b100">my</font></span> <span><font color="#0000ff">$gdb_a</font></span> = Bio::<span><font color="#006600">EnsEMBL</font></span><nowiki>::</nowiki><span><font color="#006600">Registry</font></span>-&gt;<span><font color="#006600">get_adaptor</font></span><span><font color="#66cc66">(</font></span> <span><font color="#ff0000">'Compara'</font></span>, <span><font color="#ff0000">'compara'</font></span>, <span><font color="#ff0000">'GenomeDB'</font></span> <span><font color="#66cc66">)</font></span><nowiki>;<br />
</nowiki><span>''<font color="#808080"><nowiki># genome databases setup</nowiki></font>''</span><br />
<span><font color="#b1b100">my</font></span> <span><font color="#0000ff">$edb</font></span> = <span><font color="#0000ff">$gdb_a</font></span>-&gt;<span><font color="#006600">fetch_by_name_assembly</font></span><span><font color="#66cc66">(</font></span><span><font color="#ff0000">'Caenorhabditis elegans'</font></span><span><font color="#66cc66">)</font></span><nowiki>;<br />
</nowiki><span><font color="#b1b100">my</font></span> <span><font color="#0000ff">$bdb</font></span> = <span><font color="#0000ff">$gdb_a</font></span>-&gt;<span><font color="#006600">fetch_by_name_assembly</font></span><span><font color="#66cc66">(</font></span><span><font color="#ff0000">'Caenorhabditis briggsae'</font></span><span><font color="#66cc66">)</font></span><nowiki>;<br />
</nowiki><span><font color="#b1b100">my</font></span> <span><font color="#0000ff">$rdb</font></span> = <span><font color="#0000ff">$gdb_a</font></span>-&gt;<span><font color="#006600">fetch_by_name_assembly</font></span><span><font color="#66cc66">(</font></span><span><font color="#ff0000">'Caenorhabditis remanei'</font></span><span><font color="#66cc66">)</font></span><nowiki>;<br />
<br />
<br />
</nowiki><span><font color="#b1b100">my</font></span> <span><font color="#0000ff">$method_link_species_set</font></span> = <span><font color="#0000ff">$mlssa</font></span>-&gt;<span><font color="#006600">fetch_by_method_link_type_GenomeDBs</font></span><span><font color="#66cc66">(</font></span><span><font color="#ff0000">"SYNTENY"</font></span>, <span><font color="#66cc66">[</font></span> <span><font color="#0000ff">$edb</font></span>, <span><font color="#0000ff">$bdb</font></span>, <span><font color="#0000ff">$rdb</font></span> <span><font color="#66cc66">]</font></span><span><font color="#66cc66">)</font></span><nowiki>;<br />
</nowiki><span><font color="#b1b100">my</font></span> <span><font color="#0000ff">$dnaf_a</font></span> = Bio::<span><font color="#006600">EnsEMBL</font></span><nowiki>::</nowiki><span><font color="#006600">Registry</font></span>-&gt;<span><font color="#006600">get_adaptor</font></span><span><font color="#66cc66">(</font></span> <span><font color="#ff0000">'Compara'</font></span>, <span><font color="#ff0000">'compara'</font></span>, <span><font color="#ff0000">'DnaFrag'</font></span> <span><font color="#66cc66">)</font></span><nowiki>;<br />
<br />
</nowiki><span>''<font color="#808080"><nowiki># get a DNA fragment</nowiki></font>''</span><br />
<span><font color="#b1b100">my</font></span> <span><font color="#0000ff">$dnafrag</font></span> = <span><font color="#0000ff">$dnaf_a</font></span>-&gt;<span><font color="#006600">fetch_by_GenomeDB_and_name</font></span><span><font color="#66cc66">(</font></span> <span><font color="#0000ff">$edb</font></span>, <span><font color="#ff0000">'CHROMOSOME_I'</font></span><span><font color="#66cc66">)</font></span><nowiki>;<br />
<br />
</nowiki><span><font color="#b1b100">my</font></span> <span><font color="#0000ff">$synteny_region_adaptor</font></span> = Bio::<span><font color="#006600">EnsEMBL</font></span><nowiki>::</nowiki><span><font color="#006600">Registry</font></span>-&gt;<span><font color="#006600">get_adaptor</font></span><span><font color="#66cc66">(</font></span><span><font color="#ff0000">'Compara'</font></span>, <span><font color="#ff0000">"compara"</font></span>, <span><font color="#ff0000">"SyntenyRegion"</font></span><span><font color="#66cc66">)</font></span><nowiki>;<br />
</nowiki><span><font color="#b1b100">my</font></span> <span><font color="#0000ff">$synteny_regions</font></span> = <span><font color="#0000ff">$synteny_region_adaptor</font></span>-&gt;<span><font color="#006600">fetch_by_MethodLinkSpeciesSet_DnaFrag</font></span><span><font color="#66cc66">(</font></span><span><font color="#0000ff">$method_link_species_set</font></span>,<span><font color="#0000ff">$dnafrag</font></span>, <span><font color="#cc66cc">100000</font></span>, <span><font color="#cc66cc">200000</font></span><span><font color="#66cc66">)</font></span><nowiki>;<br />
<br />
</nowiki><span><font color="#b1b100">foreach</font></span> <span><font color="#b1b100">my</font></span> <span><font color="#0000ff">$this_synteny_region</font></span> <span><font color="#66cc66">(</font></span>@<span><font color="#0000ff">$synteny_regions</font></span><span><font color="#66cc66">)</font></span> <span><font color="#66cc66">{</font></span><br />
<span><font color="#b1b100">my</font></span> <span><font color="#0000ff">$these_dnafrag_regions</font></span> = <span><font color="#0000ff">$this_synteny_region</font></span>-&gt;<span><font color="#006600">children</font></span><span><font color="#66cc66">(</font></span><span><font color="#66cc66">)</font></span><nowiki>;<br />
</nowiki><span><font color="#b1b100">foreach</font></span> <span><font color="#b1b100">my</font></span> <span><font color="#0000ff">$this_dnafrag_region</font></span> <span><font color="#66cc66">(</font></span>@<span><font color="#0000ff">$these_dnafrag_regions</font></span><span><font color="#66cc66">)</font></span> <span><font color="#66cc66">{</font></span><br />
[http://www.perldoc.com/perl5.6/pod/func/print.html <span><font color="#000066">print</font></span>] <span><font color="#0000ff">$this_dnafrag_region</font></span>-&gt;<span><font color="#006600">dnafrag</font></span>-&gt;<span><font color="#006600">genome_db</font></span>-&gt;<span><font color="#006600">name</font></span>, <span><font color="#ff0000">": "</font></span>, <span><font color="#0000ff">$this_dnafrag_region</font></span>-&gt;<span><font color="#006600">slice</font></span>-&gt;<span><font color="#006600">name</font></span>, <span><font color="#ff0000">"<span>'''<font color="#000099">\n</font>'''</span>"</font></span><nowiki>;<br />
</nowiki><span><font color="#66cc66">}</font></span><br />
[http://www.perldoc.com/perl5.6/pod/func/print.html <span><font color="#000066">print</font></span>] <span><font color="#ff0000">"<span>'''<font color="#000099">\n</font>'''</span>"</font></span><nowiki>;<br />
</nowiki><span><font color="#66cc66">}</font></span></div>
Tharris