<div id="reply-content"><div id="reply-content">Hi Guillermo,</div><div id="reply-content"><br></div><div id="reply-content">Can you try replacing that with split /\n/ or /\n|\r/?</div><div id="reply-content"><br></div><div id="reply-content">Thanks,</div><div id="reply-content">Harpreet</div></div><div id="07C342C156484D8C970265870C363F6A"><div><br></div></div>
<p style="color: #A0A0A8;">On Friday, 5 June 2015 at 11:36, Guillermo Marco Puche wrote:</p>
<blockquote type="cite" style="border-left-style:solid;border-width:1px;margin-left:0px;padding-left:10px;">
<div id="quoted-message-content"><div>
<meta content="text/html; charset=windows-1252" http-equiv="Content-Type">
Hello Will,<br>
<br>
Thank you for the info Matthew.<br>
<br>
I'm still getting lines split on my work environment.<br>
<br>
<ol>
<li><b>foreach my $line(split /\r|(?>\v|\x0D\x0A)/) {...}</b><br><blockquote>variant_effect_predictor.pl -database -i input.vcf
-o test.vcf --force_overwrite<br>
2015-06-05 12:26:14 - Starting...<br>
<b><font color="#ff0000">4.2</font></b> ("##fileformat=VCFv4.2
getting" split into "<b>4.2</b>" I putted a print in VEP.pm)<br>
2015-06-05 12:26:14 - Detected format of input file as id<br>
</blockquote></li>
<li><b>foreach my $line(split /(?>\v|\x0D\x0A)/) {...}</b><br><blockquote>same result as 1</blockquote></li>
<li><b>foreach my $line(split /\r/) {...}<br>
</b><blockquote>same result as 1 and 2</blockquote></li>
</ol>
I cannot update Perl version at this moment so I gues I will have to
completely remove this split from variant_effect_predictor.pl code.<br>
How can I update this line of code (176) to avoid any split?<br>
<br>
Regards,<br>
Guillermo.<br>
<br>
<br>
<div>On 05/06/15 10:28, Will McLaren wrote:<br>
</div><blockquote type="cite"><div>
<div dir="ltr">Thanks Matthew for the detective work.
<div><br>
</div>
<div>I've removed the \R from the split function and replaced it
with what perldoc says it is shorthand for; tests pass OK and
it seems to work on the Windows input file that prompted me to
make this change in the first place.</div>
<div><br>
</div>
<div>I've patched the fix to release/79 and release/80, so
Guillermo I'd appreciate if you could update your
ensembl-tools checkout and give this a test run for me.</div>
<div><br>
</div>
<div>Thanks everyone</div>
<div><br>
</div>
<div>Will</div>
</div>
<div><br>
<div>On 4 June 2015 at 19:17, Healy, Matthew
<span dir="ltr"><<a moz-do-not-send="true" href="mailto:Matthew.Healy@bms.com" target="_blank">Matthew.Healy@bms.com</a>></span>
wrote:<br><blockquote type="cite"><div>
<div bgcolor="white" link="blue" vlink="purple" lang="EN-US">
<div>
<p style="margin: 0px;"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span></p>
<p style="margin: 0px;"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">The
\R was added in Perl 5.10.0:</span></p>
<p style="margin: 0px;"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><a moz-do-not-send="true" href="http://perldoc.perl.org/5.10.0/perldelta.html" target="_blank">http://perldoc.perl.org/5.10.0/perldelta.html</a></span></p>
<p style="margin: 0px;"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span></p>
<p style="margin: 0px;"><b><span style="color:windowtext">Vertical and horizontal
whitespace, and linebreak</span></b><span style="color:windowtext">
</span></p>
<p style="margin: 0px;">
<span style="color:windowtext">Regular expressions now
recognize the </span><span style="font-size:10.0pt;font-family:"Courier
New";color:windowtext">\v</span><span style="color:windowtext"> and
</span><span style="font-size:10.0pt;font-family:"Courier
New";color:windowtext">\h</span><span style="color:windowtext"> escapes that match
vertical and horizontal whitespace, respectively.
</span><span style="font-size:10.0pt;font-family:"Courier
New";color:windowtext">\V</span><span style="color:windowtext"> and
</span><span style="font-size:10.0pt;font-family:"Courier
New";color:windowtext">\H</span><span style="color:windowtext"> logically match their
complements.</span></p>
<p style="margin: 0px;">
<span style="font-size:10.0pt;font-family:"Courier
New";color:windowtext">\R</span><span style="color:windowtext"> matches a generic
linebreak, that is, vertical whitespace, plus the
multi-character sequence
</span><span style="font-size:10.0pt;font-family:"Courier
New";color:windowtext">"\x0D\x0A"</span><span style="color:windowtext"> .</span></p>
<p style="margin: 0px;"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span></p>
<p style="margin: 0px;"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span></p>
<p style="margin: 0px;"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span></p>
<div>
<div style="border:none;border-top:solid #b5c4df
1.0pt;padding:3.0pt 0in 0in 0in">
<p style="margin: 0px;"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">
<a moz-do-not-send="true" href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a>
[mailto:<a moz-do-not-send="true" href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a>]
<b>On Behalf Of </b>Guillermo Marco Puche<br>
<b>Sent:</b> 04 June, 2015 2:10 PM<br>
<b>To:</b> <a moz-do-not-send="true" href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a></span></p>
<div>
<div><br>
<b>Subject:</b> Re: [ensembl-dev] VEP 79 API
problems</div>
</div>
</div>
</div>
<div>
<div>
<p style="margin: 0px;"> </p>
<div>
<p style="margin: 0px;">Yes
I guess it's clear Perl version is the problem.
I'll remove \R from this line in the script
until I can update Perl version in my work
environment.<br>
<br>
As always, thank you for your fantastic support.<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
El 04/06/2015 a las 18:19, Healy, Matthew
escribió:</p>
</div><blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p style="margin: 0px;"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">In
the regex documentation for Perl 5.8.8 there
is no mention of \R (there is of course \r
lowercase), so the Perl version probably is
the issue:</span></p>
<p style="margin: 0px;"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><a moz-do-not-send="true" href="http://perldoc.perl.org/5.8.8/perlre.html" target="_blank">http://perldoc.perl.org/5.8.8/perlre.html</a></span></p>
<p style="margin: 0px;"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span></p>
<p style="margin: 0px;"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span></p>
<div style="border:none;border-top:solid #b5c4df
1.0pt;padding:3.0pt 0in 0in 0in">
<p style="margin: 0px;"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">
<a moz-do-not-send="true" href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a>
[<a moz-do-not-send="true" href="mailto:dev-bounces@ensembl.org" target="_blank">mailto:dev-bounces@ensembl.org</a>]
<b>On Behalf Of </b>Will McLaren<br>
<b>Sent:</b> 04 June, 2015 12:12 PM<br>
<b>To:</b> Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] VEP 79 API
problems</span></p>
</div>
<p style="margin: 0px;"> </p>
<div>
<p style="margin: 0px;">I'm
wondering if 5.8.8 has different regex
handling to newer Perl versions. Someone else
in the Ensembl team may know better than me on
this one.</p>
<div>
<p style="margin: 0px;"> </p>
</div>
<div>
<p style="margin: 0px;">I
believe the Ensembl project now recommends
at least 5.10 (according to <a moz-do-not-send="true" href="http://www.ensembl.org/info/docs/api/api_installation.html" target="_blank">http://www.ensembl.org/info/docs/api/api_installation.html</a>
at least); most people in the wild use 5.14
or 5.16 AFAIK.</p>
</div>
<div>
<p style="margin: 0px;"> </p>
</div>
<div>
<p style="margin: 0px;">If
you can possibly try a newer version of Perl
this may solve your issues. Perlbrew is a
nice way to manage different versions and
module sets <a moz-do-not-send="true" href="http://perlbrew.pl/" target="_blank">http://perlbrew.pl/</a></p>
</div>
<div>
<p style="margin: 0px;"> </p>
</div>
<div>
<p style="margin: 0px;">Will</p>
</div>
</div>
<div>
<p style="margin: 0px;"> </p>
<div>
<p style="margin: 0px;">On
4 June 2015 at 17:02, Guillermo Marco Puche
<<a moz-do-not-send="true" href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>>
wrote:</p>
<div>
<p style="margin: 0px;">Hello Will,<br>
<br>
Wrong behavior machine has Centos 5.4 and
Perl v5.8.8 built for
x86_64-linux-thread-multi.<br>
<br>
So should I completly remove ?</p>
<pre style="margin-left:1.0in"><b> foreach my $line(split /\r|\R/) {</b></pre>
<p style="margin: 0px;"><br>
I was thinking about just removing \R from
regex.<br>
<br>
Regards,<br>
Guillermo.</p>
<div>
<div>
<p style="margin: 0px;">
</p>
<div>
<p style="margin: 0px;">On
04/06/15 17:49, Will McLaren wrote:</p>
</div><blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p style="margin: 0px;">Thanks </p>
<div>
<p style="margin: 0px;"> </p>
</div>
<div>
<p style="margin: 0px;">I had
forgotten about that change. You
could just edit the script and
change or even remove the
regexp:</p>
</div>
<div>
<p style="margin: 0px;"> </p>
</div>
<div>
<p style="margin: 0px;">foreach
my $line(($_)) {</p>
</div>
<div>
<p style="margin: 0px;"> </p>
</div>
<div>
<p style="margin: 0px;">What's
your Perl version and system
architecture? I'm surprised this
has not caught anyone else out.</p>
</div>
<div>
<p style="margin: 0px;"> </p>
</div>
<div>
<p style="margin: 0px;">Will</p>
</div>
</div>
<div>
<p style="margin: 0px;"> </p>
<div>
<p style="margin: 0px;">On 4
June 2015 at 14:47, Guillermo
Marco Puche <<a moz-do-not-send="true" href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>>
wrote:</p>
<div>
<p style="margin: 0px;">
Hi Will,<br>
<br>
I've been comparing
variant_effect_predictor
script from version 75 vs 79.<br>
After adding a few prints to
VEP.pm inside I've spotted the
bug. However I cannot resolve
it.<br>
<br>
Those lanes are new from 75 to
79 in VEP script (175 and
176):</p>
<pre style="margin-left:1.0in"><b> # split again to avoid Windows character nonsense</b></pre>
<pre style="margin-left:1.0in"><b> foreach my $line(split /\r|\R/) {</b></pre>
<p style="margin: 0px;"><br>
<br>
I've checked that script is
spliting line each time it
finds a capital R in VCF file
as identifying it as a newline
character from Windows. I
can't reproduce it in virtual
machine since its a fresh
Linux install. In my work
environment I'm getting this
kind of bug, so I guess it has
something to do with file
enconding or locale? Has
anyone else experienced this?<br>
<br>
Now I know where's the error
but I've no idea how to solve
it.<br>
<br>
Regards,<br>
Guillermo. </p>
<div>
<div>
<p style="margin: 0px;">
</p>
<div>
<p style="margin: 0px;">On
04/06/15 15:16, Will
McLaren wrote:</p>
</div><blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p style="margin-left:1.0in">Sorry
Guillermo, I'm running
out of ideas. </p>
<p style="margin-left:1.0in">Does
the test unit run OK?</p>
<p style="margin-left:1.0in">perl
ensembl-tools/scripts/variant_effect_predictor/t/variant_effect_predictor.t</p>
<p style="margin-left:1.0in">Will</p>
<div>
<p style="margin: 0px;">On
4 Jun 2015 12:27,
"Guillermo Marco
Puche" <<a moz-do-not-send="true" href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>>
wrote:</p>
<div>
<p style="margin: 0px;">Hi
Will,<br>
<br>
I'm getting the
exact same error
with
example_GRCh37.vcf:</p>
<pre style="margin-left:1.0in">ERROR: Could not detect input file format</pre>
<p style="margin: 0px;">
<br>
I've made a test
script as you
suggest with the
following code and I
don't get any error:</p>
<pre style="margin-left:1.0in">#!/usr/bin/env perl</pre>
<pre style="margin-left:1.0in"> </pre>
<pre style="margin-left:1.0in">use strict;</pre>
<pre style="margin-left:1.0in">use Bio::EnsEMBL::Variation::Utils::VEP qw(detect_format);</pre>
<p style="margin: 0px;">
<br>
Regards,<br>
Guillermo.</p>
<div>
<p style="margin: 0px;">On 04/06/15 13:12, Will McLaren wrote:</p>
</div><blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p style="margin-left:1.0in">Hi
again</p>
<p style="margin-left:1.0in">If
the script is not
detecting the
input format then
it is almost
certainly an issue
with the input
file. There's very
little code that
gets run to detect
the format, and
it's all internal
to the VEP code.</p>
<p style="margin-left:1.0in">You
could write a
short script to
test the method,
just import
detect_format from
Bio:EnsEMBL::Variation::Utils::VEP</p>
<p style="margin-left:1.0in">Does
it detect the
example_GRCh37.vcf
format correctly?</p>
<p style="margin-left:1.0in">The
file you shared on
Dropbox works fine
for me on my Mac
and a Linux box.
</p>
<p style="margin-left:1.0in">Will</p>
<div>
<p style="margin: 0px;">On 4 Jun 2015 10:44, "Guillermo Marco Puche"
<<a moz-do-not-send="true" href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>>
wrote:</p>
<div>
<p style="margin: 0px;">
Hi again Will,<br>
<br>
I'm trying
with latest
ensembl 80.<br>
If I don't
specify <b>-format
vcf</b> I get
the following
error:</p>
<pre style="margin-left:1.0in">perl ensembl-tools/scripts/variant_effect_predictor/<a moz-do-not-send="true" href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> -i input.vcf -database --force_overwrite</pre>
<pre style="margin-left:1.0in">2015-06-04 11:36:59 - Starting...</pre>
<pre style="margin-left:1.0in">ERROR: Could not detect input file format</pre>
<p style="margin: 0px;">
<br>
If I force
format with<b>
-format vcf </b>I
get all the
errors. (see
error log
attached). I'm
using the same
input.vcf file
I posted
yesterday.<br>
Just to
discard it's
not VCF, I've
installed a
fresh linux on
virtual
machine and
just cloned
and setup
Ensembl and
Bioperl. On
fresh Linux
install I was
only asked to
install MySQL
perl module (I
installed it
via CPAN).<br>
It's working
like a cake. <br>
<br>
I discard
there's a
problem with
the input VCF
because I'm
using exactly
the input over
the two
environments
(and the same
one you used
to test it
yesterday)
<br>
<br>
So my question
is: Does VEP
script use any
other library,
environment
variable or
tool which may
be
interfering?<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
<br>
</p>
<div>
<p style="margin: 0px;">On 04/06/15 09:32, Guillermo Marco Puche
wrote:</p>
</div><blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p style="margin: 0px;">
Hi again Will,<br>
<br>
I've completly
cleaned
PERL5LIB
environment
var. I've been
testing
changing
between
bioperl 1.2.3
and bioperl
1.6.1 and got
same
warnings/errors.<br>
I've cloned
again all 79
API like you
suggested in a
new tmp
location and
included it in
$PERL5LIB.</p>
<pre style="margin-left:1.0in"><b>echo $PERL5LIB </b></pre>
<p style="margin: 0px;">
/share/apps/local/bioperl-live:/share/gluster/tests/gmarco/tmp/ensembl/modules:/share/gluster/tests/gmarco/tmp/ensembl-funcgen/modules:/share/gluster/tests/gmarco/tmp/ensembl-variation/modules</p>
<pre style="margin-left:1.0in"><b>ll /share/gluster/tests/gmarco/tmp</b></pre>
<p style="margin: 0px;">
total 20<br>
drwxrwxr-x 8
gmarco users
4096 jun 4
08:44 ensembl<br>
drwxrwxr-x 8
gmarco users
146 jun 4
08:46
ensembl-funcgen<br>
drwxrwxr-x 5
gmarco users
64 jun 4
08:43
ensembl-tools<br>
drwxrwxr-x 10
gmarco users
4096 jun 4
08:45
ensembl-variation</p>
<pre style="margin-left:1.0in"><b>perl ensembl-tools/scripts/variant_effect_predictor/<a moz-do-not-send="true" href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> -i input.vcf -database --force_overwrite</b></pre>
<p style="margin: 0px;">
2015-06-04
09:29:13 -
Starting...<br>
ERROR: Could
not detect
input file
format<br>
<br>
If use the
following
flags <b>-format
vcf</b> <b>-vcf
</b>then I
start getting
all those
errors (see
yesterday
log).<br>
<br>
Is there any
other Perl lib
or requirement
I could be
missing? As I
said it's very
weird I have 0
problems with
Ensembl 75
local API.<br>
<br>
Best regards,<br>
Guillermo.</p>
<div>
<p style="margin: 0px;">On 03/06/15 18:14, Will McLaren wrote:</p>
</div><blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p style="margin: 0px;">Hi again, </p>
<div>
<p style="margin: 0px;"> </p>
</div>
<div>
<p style="margin: 0px;">I can't recreate the problem with that input
file I'm
afraid, either
on my normal
setup or
scrubbing
PERL5LIB and
starting from
scratch.</p>
</div>
<div>
<p style="margin: 0px;"> </p>
</div>
<div>
<p style="margin: 0px;">See commands I used and input below.</p>
</div>
<div>
<p style="margin: 0px;"> </p>
</div>
<div>
<p style="margin: 0px;">Perhaps you haven't got release/79 of
ensembl-tools
too?</p>
</div>
<div>
<p style="margin: 0px;"> </p>
</div>
<div>
<p style="margin: 0px;">Have you tried running the installer from
within
ensembl-tools/scripts/variant_effect_predictor?
This shouldn't
affect your
PERL5LIB or
other git
checkouts.</p>
</div>
<div>
<p style="margin: 0px;"> </p>
</div>
<div>
<p style="margin: 0px;">Will</p>
</div>
<div>
<p style="margin: 0px;"> </p>
</div>
<div>
<p style="margin: 0px;">===================</p>
</div>
<div>
<p style="margin: 0px;"> </p>
</div>
<div>
<p style="margin: 0px;">mkdir ~/src/tmp</p>
</div>
<div>
<p style="margin: 0px;">cd ~/src/tmp</p>
</div>
<div>
<p style="margin: 0px;">git clone --branch release/79 <a moz-do-not-send="true" href="https://github.com/Ensembl/ensembl-tools.git" target="_blank">
https://github.com/Ensembl/ensembl-tools.git</a></p>
</div>
<div>
<p style="margin: 0px;">git clone --branch release/79 <a moz-do-not-send="true" href="https://github.com/Ensembl/ensembl.git" target="_blank">
https://github.com/Ensembl/ensembl.git</a></p>
</div>
<div>
<p style="margin: 0px;">git clone --branch release/79 <a moz-do-not-send="true" href="https://github.com/Ensembl/ensembl-variation.git" target="_blank">
https://github.com/Ensembl/ensembl-variation.git</a></p>
</div>
<div>
<p style="margin: 0px;">git clone --branch release/79 <a moz-do-not-send="true" href="https://github.com/Ensembl/ensembl-funcgen.git" target="_blank">
https://github.com/Ensembl/ensembl-funcgen.git</a></p>
</div>
<div>
<p style="margin: 0px;">export
PERL5LIB=ensembl/modules:ensembl-variation/modules:ensembl-funcgen/modules:/Users/will/src/bioperl-1.2.3/:/Users/will/src/lib/perl5/</p>
</div>
<div>
<div>
<p style="margin: 0px;">perl
ensembl-tools/scripts/variant_effect_predictor/<a moz-do-not-send="true" href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a>
-i
~/Downloads/input.vcf
-database</p>
</div>
<div>
<p style="margin: 0px;">2015-06-03 17:09:54 - Starting...</p>
</div>
<div>
<p style="margin: 0px;">2015-06-03 17:09:54 - Detected format of input
file as vcf</p>
</div>
<div>
<p style="margin: 0px;">2015-06-03 17:09:54 - Read 1 variants into
buffer</p>
</div>
<div>
<p style="margin: 0px;">2015-06-03 17:09:54 - Reading transcript data
from cache
and/or
database</p>
</div>
<div>
<p style="margin: 0px;">[================================================================================================================================]
[ 100% ]</p>
</div>
<div>
<p style="margin: 0px;">2015-06-03 17:10:00 - Retrieved 7 transcripts
(0 mem, 0
cached, 7 DB,
0 duplicates)</p>
</div>
<div>
<p style="margin: 0px;">2015-06-03 17:10:00 - Analyzing chromosome 1</p>
</div>
<div>
<p style="margin: 0px;">2015-06-03 17:10:00 - Analyzing variants</p>
</div>
<div>
<p style="margin: 0px;">[================================================================================================================================]
[ 100% ]</p>
</div>
<div>
<p style="margin: 0px;">2015-06-03 17:10:00 - Calculating consequences</p>
</div>
<div>
<p style="margin: 0px;">2015-06-03 17:10:00 - Processed 1 total
variants (0
vars/sec, 0
vars/sec
total)</p>
</div>
<div>
<p style="margin: 0px;">2015-06-03 17:10:00 - Wrote stats summary to
variant_effect_output.txt_summary.html</p>
</div>
<div>
<p style="margin: 0px;">2015-06-03 17:10:00 - Finished!</p>
</div>
</div>
<div>
<p style="margin: 0px;"> </p>
</div>
<div>
<p style="margin: 0px;"> </p>
</div>
<div>
<p style="margin: 0px;"> </p>
</div>
</div>
<div>
<p style="margin: 0px;"> </p>
<div>
<p style="margin: 0px;">On 3 June 2015 at 16:51, Guillermo Marco Puche
<<a moz-do-not-send="true" href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>>
wrote:</p>
<div>
<p style="margin: 0px;">Hi Will,<br>
<br>
I've been
checking and I
can't see any
unintended
whitespace or
problem with
tabulations.<br>
I've no issues
with old vep
75 script and
API. I've
updated the
Bioperl lib in
$PERL5LIB
variable from
1.2.3 to 1.6.1
(I didn't see
this change
before sorry)
however I'm
still getting
all those
errors.<br>
<br>
Here's a link
where you can
download the
VCF I'm using
as input: <a moz-do-not-send="true" href="https://www.dropbox.com/sh/felwyoo5kl2mgty/AAC177Digqy-_mEmyk9WvmYba/input.vcf?dl=0" target="_blank">
https://www.dropbox.com/sh/felwyoo5kl2mgty/AAC177Digqy-_mEmyk9WvmYba/input.vcf?dl=0</a><br>
<br>
Thank you.<br>
<br>
Best regards,<br>
Guille. </p>
<div>
<div>
<p style="margin: 0px;">
</p>
<div>
<p style="margin: 0px;">On 03/06/15 17:30, Will McLaren wrote:</p>
</div><blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p style="margin: 0px;">Hi Guille, </p>
<div>
<p style="margin: 0px;"><br>
It looks to me
like your
input is not
being parsed
properly.</p>
</div>
<div>
<p style="margin: 0px;"> </p>
</div>
<div>
<p style="margin: 0px;">Check the formatting of your input VCF; double
check that it
is valid VCF,
and that you
haven't got
any unintended
whitespace on
any of the
lines.</p>
</div>
<div>
<p style="margin: 0px;"> </p>
</div>
<div>
<p style="margin: 0px;">If you still have an issue, can you send a
line or two of
the input that
recreates
these issues?</p>
</div>
<div>
<p style="margin: 0px;"> </p>
</div>
<div>
<p style="margin: 0px;">Thanks</p>
</div>
<div>
<p style="margin: 0px;"> </p>
</div>
<div>
<p style="margin: 0px;">Will McLaren</p>
</div>
<div>
<p style="margin: 0px;">Ensembl Variation</p>
</div>
<div>
<p style="margin: 0px;"> </p>
</div>
</div>
<div>
<p style="margin: 0px;"> </p>
<div>
<p style="margin: 0px;">On 3 June 2015 at 16:16, Guillermo Marco Puche
<<a moz-do-not-send="true" href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>>
wrote:</p>
<div>
<p style="margin: 0px;">Dear devs,<br>
<br>
I'm trying
ensembl 79
VEP.<br>
<br>
This is my
dummy input
VCF: <a moz-do-not-send="true" href="http://pastebin.com/kFKWH50q" target="_blank">
http://pastebin.com/kFKWH50q#</a><br>
<br>
I've cloned
and installed
API from
github as
always (this
step is
repeated for
variaton,
funcgen and
compara):</p>
<p style="margin: 0px;">
<span style="font-size:10.0pt;font-family:Symbol"><span>·<span style="font:7.0pt
"Times
New
Roman"">
</span></span></span>git
clone --branch
release/79 <a moz-do-not-send="true" href="https://github.com/Ensembl/ensembl.git" target="_blank">
<span style="color:#5c3566">https://github.com/Ensembl/ensembl.git</span></a>
ensembl_79</p>
<p style="margin-left:1.0in">PERL5LIB
env variable
is correctly
pointing to
the cloned
API:
</p>
<p style="margin: 0px;">
<span style="font-size:10.0pt;font-family:Symbol"><span>·<span style="font:7.0pt
"Times
New
Roman"">
</span></span></span>echo
$PERL5LIB <br>
/share/apps/local/bioperl-live:/share/apps/src/ensembl_79/modules:/share/apps/src/ensembl_79-compara/modules:/share/apps/src/ensembl_79-variation/modules:/share/apps/src/ensembl_79-functgenomics/modules</p>
<p style="margin-left:1.0in">However
I'm getting a
lot of errors
I really don't
understand. It
seems like a
bug with API
installation
with me. If I
change
$PERL5LIB
variable to
point to 75
API (previous
version I was
using) I can't
reproduce the
errors VEP
script works
for this old
75 version.</p>
<p style="margin-left:1.0in">I've
been reading
the docs again
and I can't
seen any
additional
PERL library
requirement.</p>
<p style="margin-left:1.0in">Here's
the error log:
<a moz-do-not-send="true" href="http://pastebin.com/VvQrkEQZ" target="_blank">
http://pastebin.com/VvQrkEQZ</a></p>
<p style="margin-left:1.0in"><br>
Thank you!</p>
<p style="margin-left:1.0in">Best
regards,<br>
Guille.</p>
</div>
<p style="margin: 0px;">
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