tag:treefam.tenderapp.com,2013-02-16:/discussions/problems/40-issues-with-some-of-the-tfs-and-perl-api-get_familiespl-scriptTreeFam: Discussion 2020-06-16T16:08:31Ztag:treefam.tenderapp.com,2013-02-16:Comment/370182262015-06-09T15:03:50Z2015-06-09T15:03:50ZIssues with some of the TFs and perl API get_families.pl script<div><p>Hi Patrick,</p>
<p>The TreeFam 9 database is using the database schema from Ensembl
Compara 69, not 70. The e70 code is expecting a gene_align_id
column which was not present in e69</p>
<p>Can you please select the "release/69" branch and try again
?</p>
<p>Matthieu</p></div>Matthieu Muffatotag:treefam.tenderapp.com,2013-02-16:Comment/370182262015-06-09T16:05:40Z2015-06-09T16:05:40ZIssues with some of the TFs and perl API get_families.pl script<div><p>Thanks... i'll try that. When i originally ran the script using
ensembl 79,<br>
i received an error:</p>
<p>For treefam_production_9_69 there is a difference in the
software release<br>
(79) and the database release (70). You should update one of these
to ensure that your script does not crash.</p>
<p>I assumed that meant i should use Ensembl Compara 70</p></div>Patrick McGrathtag:treefam.tenderapp.com,2013-02-16:Comment/370182262015-06-09T16:09:45Z2015-06-09T16:09:45ZIssues with some of the TFs and perl API get_families.pl script<div><p>That was a sensible decision :)<br>
I've looked at the database and there is conflicting information in
the table that reports the schema version. It both says 69 and
70.</p>
<p>v69 has been used to produce the database, and should be used to
read from it. I'll look into removing the bit that says 70.You can
discard the warning in the meantime</p>
<p>Matthieu</p></div>Matthieu Muffatotag:treefam.tenderapp.com,2013-02-16:Comment/370182262017-09-27T01:19:47Z2017-09-27T01:19:49ZIssues with some of the TFs and perl API get_families.pl script<div><p>I was curious if this issue was ever determined (i.e. some of the Treefams identified by the treefam_scan.pl script (such as TF314013) do not have tree files available in the download section of this website.</p>
<p>I can use the MySQL database to get a newick format file for TF314013, however, it appears to lack support values for each node unlike the treefiles hosted on this web server. Is there a way to get the phylogeny files for TF314013 and the other missing treefams that include node support values?</p>
<p>Thanks....</p></div>Patrick McGrathtag:treefam.tenderapp.com,2013-02-16:Comment/370182262017-10-02T13:19:51Z2017-10-02T13:19:51ZIssues with some of the TFs and perl API get_families.pl script<div><p>This is because of the way data have been generated for TF314013. The family (as others) was too big to directly be built (alignment, trees, orthologues), so it had to be broken down into smaller pieces (sub-families). As a result TF314013 doesn't have the same set of annotations as smaller families.</p>
<p>415 families are affected. They have the tree_type "supertree" in the database</p>
<p>Matthieu</p></div>Matthieu Muffatotag:treefam.tenderapp.com,2013-02-16:Comment/370182262017-10-02T14:24:27Z2017-10-02T14:24:28ZIssues with some of the TFs and perl API get_families.pl script<div><p>Thanks.... so what should you do if a the hmmscan hits one of these trees?<br>
How do you know which subfamily to use?</p></div>Patrick McGrathtag:treefam.tenderapp.com,2013-02-16:Comment/370182262017-10-16T12:01:45Z2017-10-16T12:01:45ZIssues with some of the TFs and perl API get_families.pl script<div><p>With the Perl API, one can fetch a tree for TF314013 that contains all the subfamilies.<br>
As this stands, the subfamilies are just the product of our own limitation when computing the alignment, trees, etc, and displaying them. The only family that ought to be used is TF314013.</p></div>Matthieu Muffato