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Hello<br>
<br>
Whilst looking into Stuart's question I looked at the variants on
chromosome 1 out of curiosity and found that most of them don't have
sift/polyphen data.<br>
Is this correct or have i made a mistake in my understanding of the
schema<br>
<br>
variants on chr1 (seq_region_id = 27511)
<br>
============================
<br>
<br>
mysql> select count(*) from transcript_variation tv inner join
<br>
homo_sapiens_core_62_37g.transcript_stable_id st on st.stable_id =
<br>
tv.feature_stable_id inner join homo_sapiens_core_62_37g.transcript
t on
<br>
t.transcript_id = st.transcript_id where t.seq_region_id = 27511;
<br>
+----------+
<br>
| count(*) |
<br>
+----------+
<br>
| 9633745 |
<br>
+----------+
<br>
1 row in set (3.34 sec)
<br>
<br>
<br>
variants on chr1 without sift and polyphen
<br>
===========================
<br>
<br>
mysql> select count(*) from transcript_variation tv inner join
<br>
homo_sapiens_core_62_37g.transcript_stable_id st on st.stable_id =
<br>
tv.feature_stable_id inner join homo_sapiens_core_62_37g.transcript
t on
<br>
t.transcript_id = st.transcript_id where t.seq_region_id = 27511 and
<br>
tv.sift_prediction is null and tv.polyphen_prediction is null;
<br>
+----------+
<br>
| count(*) |
<br>
+----------+
<br>
| 9562313 |
<br>
+----------+
<br>
1 row in set (11.22 sec)
<br>
<br>
<br>
variants on chr1 with sift and polyphen
<br>
=========================
<br>
<br>
mysql> select count(*) from transcript_variation tv inner join
<br>
homo_sapiens_core_62_37g.transcript_stable_id st on st.stable_id =
<br>
tv.feature_stable_id inner join homo_sapiens_core_62_37g.transcript
t on
<br>
t.transcript_id = st.transcript_id where t.seq_region_id = 27511 and
<br>
tv.sift_prediction is not null and tv.polyphen_prediction is not
null;
<br>
+----------+
<br>
| count(*) |
<br>
+----------+
<br>
| 67919 |
<br>
+----------+
<br>
1 row in set (11.19 sec)
<br>
<br>
<br>
<br>
thanks<br>
<br>
<br>
On 17/05/11 13:59, Stuart Meacham wrote:
<blockquote cite="mid:4DD27121.7010404@cam.ac.uk" type="cite">Hello,
<br>
<br>
Thanks for the reply.
<br>
<br>
On 17/05/11 13:35, Will McLaren wrote:
<br>
<br>
<blockquote type="cite">
<br>
This is strange - are you sure you are checking out the branch
and not
<br>
the head of the API? You should be doing something like:
<br>
<br>
cvs checkout -r branch-ensembl-62 ensembl
<br>
cvs checkout -r branch-ensembl-62 ensembl-variation
<br>
</blockquote>
<br>
Actually I just used the links from the site here:
<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/api/api_installation.html">http://www.ensembl.org/info/docs/api/api_installation.html</a>
<br>
<br>
the link(s) resolve to things like:
<br>
<br>
<a class="moz-txt-link-freetext" href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl.tar.gz?root=ensembl&only_with_tag=branch-ensembl-62&view=tar">http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl.tar.gz?root=ensembl&only_with_tag=branch-ensembl-62&view=tar</a>
<br>
<br>
<blockquote type="cite">
<br>
<blockquote type="cite">
<br>
The script silently over-writes an existing output file of the
same name,
<br>
this seems a bit brutal, perhaps the default should be to fail
if the file
<br>
exists.
<br>
</blockquote>
<br>
I think this is pretty standard behaviour for command-line
programs. I
<br>
could change it to only run if in an output file name is
specified
<br>
perhaps?
<br>
</blockquote>
<br>
Yes, probably it's standard behaviour. I was just imagining
accidentally overwriting a file the script had spent 24 hours
creating . . .
<br>
<br>
<blockquote type="cite">
<br>
That's also odd - any variants classified as non-synonymous
coding
<br>
should have a "SIFT=*" entry in the final column. Can you try
the
<br>
attached file as input on your system?
<br>
<br>
</blockquote>
<br>
No problem, the command I used was:
<br>
<br>
perl ./variant_effect_predictor_2.pl -r reg.pl -i ./test.txt -w -b
100000 --sift=p --polyphen=p --failed=0 -terms=so
<br>
<br>
and the output (no errors but also no predictions) is attached.
<br>
<br>
Cheers
<br>
<br>
Stuart
<br>
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