[ensembl-dev] VEP 79 API problems

Guillermo Marco Puche guillermo.marco at sistemasgenomicos.com
Fri Jun 5 13:51:48 BST 2015


Hi Harpreet,

I've instead updated Perl to latest version.
I got some of my plugins outdated but that's a totally different and 
independent problem.

I'm getting this warning when executing vep script without 
"*--no_progress*" option:

Negative repeat count does nothing at 
/share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm 
line 6247, <GEN0> line 134.

Now I'm in a hurry I'll try \n in split on Monday and report back.

Regards,
Guillermo.

On 05/06/15 14:34, Harpreet Riat wrote:
> Hi Guillermo,
>
> Can you try replacing that with split /\n/ or /\n|\r/?
>
> Thanks,
> Harpreet
>
> On Friday, 5 June 2015 at 11:36, Guillermo Marco Puche wrote:
>
>> Hello Will,
>>
>> Thank you for the info Matthew.
>>
>> I'm still getting lines split on my work environment.
>>
>>  1. *foreach my $line(split /\r|(?>\v|\x0D\x0A)/) {...}*
>>
>>         variant_effect_predictor.pl -database -i input.vcf -o
>>         test.vcf --force_overwrite
>>         2015-06-05 12:26:14 - Starting...
>>         *4.2* ("##fileformat=VCFv4.2 getting" split into "*4.2*" I
>>         putted a print in VEP.pm)
>>         2015-06-05 12:26:14 - Detected format of input file as id
>>
>>  2. *foreach my $line(split /(?>\v|\x0D\x0A)/) {...}*
>>
>>         same result as 1
>>
>>  3. *foreach my $line(split /\r/) {...}
>>     *
>>
>>         same result as 1 and 2
>>
>> 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.
>> How can I update this line of code (176) to avoid any split?
>>
>> Regards,
>> Guillermo.
>>
>>
>> On 05/06/15 10:28, Will McLaren wrote:
>>> Thanks Matthew for the detective work.
>>>
>>> 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.
>>>
>>> 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.
>>>
>>> Thanks everyone
>>>
>>> Will
>>>
>>> On 4 June 2015 at 19:17, Healy, Matthew <Matthew.Healy at bms.com 
>>> <mailto:Matthew.Healy at bms.com>> wrote:
>>>>
>>>> The \R was added in Perl 5.10.0:
>>>>
>>>> http://perldoc.perl.org/5.10.0/perldelta.html
>>>>
>>>> *Vertical and horizontal whitespace, and linebreak*
>>>>
>>>> Regular expressions now recognize the \vand \hescapes that match 
>>>> vertical and horizontal whitespace, respectively. \Vand \Hlogically 
>>>> match their complements.
>>>>
>>>> \Rmatches a generic linebreak, that is, vertical whitespace, plus 
>>>> the multi-character sequence "\x0D\x0A".
>>>>
>>>> *From:*dev-bounces at ensembl.org <mailto:dev-bounces at ensembl.org> 
>>>> [mailto:dev-bounces at ensembl.org <mailto:dev-bounces at ensembl.org>] 
>>>> *On Behalf Of *Guillermo Marco Puche
>>>> *Sent:* 04 June, 2015 2:10 PM
>>>> *To:* dev at ensembl.org <mailto:dev at ensembl.org>
>>>>
>>>>
>>>> *Subject:* Re: [ensembl-dev] VEP 79 API problems
>>>>
>>>> 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.
>>>>
>>>> As always, thank you for your fantastic support.
>>>>
>>>> Best regards,
>>>> Guillermo.
>>>>
>>>> El 04/06/2015 a las 18:19, Healy, Matthew escribió:
>>>>
>>>>     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:
>>>>
>>>>     http://perldoc.perl.org/5.8.8/perlre.html
>>>>
>>>>     *From:*dev-bounces at ensembl.org <mailto:dev-bounces at ensembl.org>
>>>>     [mailto:dev-bounces at ensembl.org] *On Behalf Of *Will McLaren
>>>>     *Sent:* 04 June, 2015 12:12 PM
>>>>     *To:* Ensembl developers list
>>>>     *Subject:* Re: [ensembl-dev] VEP 79 API problems
>>>>
>>>>     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.
>>>>
>>>>     I believe the Ensembl project now recommends at least 5.10
>>>>     (according to
>>>>     http://www.ensembl.org/info/docs/api/api_installation.html at
>>>>     least); most people in the wild use 5.14 or 5.16 AFAIK.
>>>>
>>>>     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 http://perlbrew.pl/
>>>>
>>>>     Will
>>>>
>>>>     On 4 June 2015 at 17:02, Guillermo Marco Puche
>>>>     <guillermo.marco at sistemasgenomicos.com
>>>>     <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>>>>
>>>>     Hello Will,
>>>>
>>>>     Wrong behavior machine has Centos 5.4 and Perl v5.8.8 built for
>>>>     x86_64-linux-thread-multi.
>>>>
>>>>     So should I completly remove ?
>>>>
>>>>     *  foreach my $line(split /\r|\R/) {*
>>>>
>>>>
>>>>     I was thinking about just removing \R from regex.
>>>>
>>>>     Regards,
>>>>     Guillermo.
>>>>
>>>>     On 04/06/15 17:49, Will McLaren wrote:
>>>>
>>>>         Thanks
>>>>
>>>>         I had forgotten about that change. You could just edit the
>>>>         script and change or even remove the regexp:
>>>>
>>>>         foreach my $line(($_)) {
>>>>
>>>>         What's your Perl version and system architecture? I'm
>>>>         surprised this has not caught anyone else out.
>>>>
>>>>         Will
>>>>
>>>>         On 4 June 2015 at 14:47, Guillermo Marco Puche
>>>>         <guillermo.marco at sistemasgenomicos.com
>>>>         <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>>>>
>>>>         Hi Will,
>>>>
>>>>         I've been comparing variant_effect_predictor script from
>>>>         version 75 vs 79.
>>>>         After adding a few prints to VEP.pm inside I've spotted the
>>>>         bug. However I cannot resolve it.
>>>>
>>>>         Those lanes are new from 75 to 79 in VEP script (175 and 176):
>>>>
>>>>         *     # split again to avoid Windows character nonsense*
>>>>
>>>>         *     foreach my $line(split /\r|\R/) {*
>>>>
>>>>
>>>>
>>>>         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?
>>>>
>>>>         Now I know where's the error but I've no idea how to solve it.
>>>>
>>>>         Regards,
>>>>         Guillermo.
>>>>
>>>>         On 04/06/15 15:16, Will McLaren wrote:
>>>>
>>>>             Sorry Guillermo, I'm running out of ideas.
>>>>
>>>>             Does the test unit run OK?
>>>>
>>>>             perl
>>>>             ensembl-tools/scripts/variant_effect_predictor/t/variant_effect_predictor.t
>>>>
>>>>             Will
>>>>
>>>>             On 4 Jun 2015 12:27, "Guillermo Marco Puche"
>>>>             <guillermo.marco at sistemasgenomicos.com
>>>>             <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>>>>
>>>>             Hi Will,
>>>>
>>>>             I'm getting the exact same error with example_GRCh37.vcf:
>>>>
>>>>             ERROR: Could not detect input file format
>>>>
>>>>
>>>>             I've made a test script as you suggest with the
>>>>             following code and I don't get any error:
>>>>
>>>>             #!/usr/bin/env perl
>>>>
>>>>               
>>>>
>>>>             use strict;
>>>>
>>>>             use Bio::EnsEMBL::Variation::Utils::VEP qw(detect_format);
>>>>
>>>>
>>>>             Regards,
>>>>             Guillermo.
>>>>
>>>>             On 04/06/15 13:12, Will McLaren wrote:
>>>>
>>>>                 Hi again
>>>>
>>>>                 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.
>>>>
>>>>                 You could write a short script to test the method,
>>>>                 just import detect_format from
>>>>                 Bio:EnsEMBL::Variation::Utils::VEP
>>>>
>>>>                 Does it detect the example_GRCh37.vcf format correctly?
>>>>
>>>>                 The file you shared on Dropbox works fine for me on
>>>>                 my Mac and a Linux box.
>>>>
>>>>                 Will
>>>>
>>>>                 On 4 Jun 2015 10:44, "Guillermo Marco Puche"
>>>>                 <guillermo.marco at sistemasgenomicos.com
>>>>                 <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>>>>
>>>>                 Hi again Will,
>>>>
>>>>                 I'm trying with latest ensembl 80.
>>>>                 If I don't specify *-format vcf* I get the
>>>>                 following error:
>>>>
>>>>                 perl ensembl-tools/scripts/variant_effect_predictor/variant_effect_predictor.pl  <http://variant_effect_predictor.pl>  -i input.vcf -database --force_overwrite
>>>>
>>>>                 2015-06-04 11:36:59 - Starting...
>>>>
>>>>                 ERROR: Could not detect input file format
>>>>
>>>>
>>>>                 If I force format with*-format vcf *I get all the
>>>>                 errors. (see error log attached). I'm using the
>>>>                 same input.vcf file I posted yesterday.
>>>>                 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).
>>>>                 It's working like a cake.
>>>>
>>>>                 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)
>>>>
>>>>                 So my question is: Does VEP script use any other
>>>>                 library, environment variable or tool which may be
>>>>                 interfering?
>>>>
>>>>                 Best regards,
>>>>                 Guillermo.
>>>>
>>>>
>>>>                 On 04/06/15 09:32, Guillermo Marco Puche wrote:
>>>>
>>>>                     Hi again Will,
>>>>
>>>>                     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.
>>>>                     I've cloned again all 79 API like you suggested
>>>>                     in a new tmp location and included it in $PERL5LIB.
>>>>
>>>>                     *echo $PERL5LIB*
>>>>
>>>>                     /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
>>>>
>>>>                     *ll /share/gluster/tests/gmarco/tmp*
>>>>
>>>>                     total 20
>>>>                     drwxrwxr-x  8 gmarco users 4096 jun  4 08:44
>>>>                     ensembl
>>>>                     drwxrwxr-x  8 gmarco users 146 jun  4 08:46
>>>>                     ensembl-funcgen
>>>>                     drwxrwxr-x  5 gmarco users 64 jun  4 08:43
>>>>                     ensembl-tools
>>>>                     drwxrwxr-x 10 gmarco users 4096 jun  4 08:45
>>>>                     ensembl-variation
>>>>
>>>>                     *perl ensembl-tools/scripts/variant_effect_predictor/variant_effect_predictor.pl  <http://variant_effect_predictor.pl>  -i input.vcf -database --force_overwrite*
>>>>
>>>>                     2015-06-04 09:29:13 - Starting...
>>>>                     ERROR: Could not detect input file format
>>>>
>>>>                     If use the following flags *-format vcf* *-vcf
>>>>                     *then I start getting all those errors (see
>>>>                     yesterday log).
>>>>
>>>>                     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.
>>>>
>>>>                     Best regards,
>>>>                     Guillermo.
>>>>
>>>>                     On 03/06/15 18:14, Will McLaren wrote:
>>>>
>>>>                         Hi again,
>>>>
>>>>                         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.
>>>>
>>>>                         See commands I used and input below.
>>>>
>>>>                         Perhaps you haven't got release/79 of
>>>>                         ensembl-tools too?
>>>>
>>>>                         Have you tried running the installer from
>>>>                         within
>>>>                         ensembl-tools/scripts/variant_effect_predictor?
>>>>                         This shouldn't affect your PERL5LIB or
>>>>                         other git checkouts.
>>>>
>>>>                         Will
>>>>
>>>>                         ===================
>>>>
>>>>                         mkdir ~/src/tmp
>>>>
>>>>                         cd ~/src/tmp
>>>>
>>>>                         git clone --branch release/79
>>>>                         https://github.com/Ensembl/ensembl-tools.git
>>>>
>>>>                         git clone --branch release/79
>>>>                         https://github.com/Ensembl/ensembl.git
>>>>
>>>>                         git clone --branch release/79
>>>>                         https://github.com/Ensembl/ensembl-variation.git
>>>>
>>>>                         git clone --branch release/79
>>>>                         https://github.com/Ensembl/ensembl-funcgen.git
>>>>
>>>>                         export
>>>>                         PERL5LIB=ensembl/modules:ensembl-variation/modules:ensembl-funcgen/modules:/Users/will/src/bioperl-1.2.3/:/Users/will/src/lib/perl5/
>>>>
>>>>                         perl
>>>>                         ensembl-tools/scripts/variant_effect_predictor/variant_effect_predictor.pl
>>>>                         <http://variant_effect_predictor.pl>  -i
>>>>                         ~/Downloads/input.vcf  -database
>>>>
>>>>                         2015-06-03 17:09:54 - Starting...
>>>>
>>>>                         2015-06-03 17:09:54 - Detected format of
>>>>                         input file as vcf
>>>>
>>>>                         2015-06-03 17:09:54 - Read 1 variants into
>>>>                         buffer
>>>>
>>>>                         2015-06-03 17:09:54 - Reading transcript
>>>>                         data from cache and/or database
>>>>
>>>>                         [================================================================================================================================]
>>>>                          [ 100% ]
>>>>
>>>>                         2015-06-03 17:10:00 - Retrieved 7
>>>>                         transcripts (0 mem, 0 cached, 7 DB, 0
>>>>                         duplicates)
>>>>
>>>>                         2015-06-03 17:10:00 - Analyzing chromosome 1
>>>>
>>>>                         2015-06-03 17:10:00 - Analyzing variants
>>>>
>>>>                         [================================================================================================================================]
>>>>                          [ 100% ]
>>>>
>>>>                         2015-06-03 17:10:00 - Calculating consequences
>>>>
>>>>                         2015-06-03 17:10:00 - Processed 1 total
>>>>                         variants (0 vars/sec, 0 vars/sec total)
>>>>
>>>>                         2015-06-03 17:10:00 - Wrote stats summary
>>>>                         to variant_effect_output.txt_summary.html
>>>>
>>>>                         2015-06-03 17:10:00 - Finished!
>>>>
>>>>                         On 3 June 2015 at 16:51, Guillermo Marco
>>>>                         Puche
>>>>                         <guillermo.marco at sistemasgenomicos.com
>>>>                         <mailto:guillermo.marco at sistemasgenomicos.com>>
>>>>                         wrote:
>>>>
>>>>                         Hi Will,
>>>>
>>>>                         I've been checking and I can't see any
>>>>                         unintended whitespace or problem with
>>>>                         tabulations.
>>>>                         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.
>>>>
>>>>                         Here's a link where you can download the
>>>>                         VCF I'm using as input:
>>>>                         https://www.dropbox.com/sh/felwyoo5kl2mgty/AAC177Digqy-_mEmyk9WvmYba/input.vcf?dl=0
>>>>
>>>>                         Thank you.
>>>>
>>>>                         Best regards,
>>>>                         Guille.
>>>>
>>>>                         On 03/06/15 17:30, Will McLaren wrote:
>>>>
>>>>                             Hi Guille,
>>>>
>>>>
>>>>                             It looks to me like your input is not
>>>>                             being parsed properly.
>>>>
>>>>                             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.
>>>>
>>>>                             If you still have an issue, can you
>>>>                             send a line or two of the input that
>>>>                             recreates these issues?
>>>>
>>>>                             Thanks
>>>>
>>>>                             Will McLaren
>>>>
>>>>                             Ensembl Variation
>>>>
>>>>                             On 3 June 2015 at 16:16, Guillermo
>>>>                             Marco Puche
>>>>                             <guillermo.marco at sistemasgenomicos.com
>>>>                             <mailto:guillermo.marco at sistemasgenomicos.com>>
>>>>                             wrote:
>>>>
>>>>                             Dear devs,
>>>>
>>>>                             I'm trying ensembl 79 VEP.
>>>>
>>>>                             This is my dummy input VCF:
>>>>                             http://pastebin.com/kFKWH50q#
>>>>                             <http://pastebin.com/kFKWH50q>
>>>>
>>>>                             I've cloned and installed API from
>>>>                             github as always (this step is repeated
>>>>                             for variaton, funcgen and compara):
>>>>
>>>>                             ·git clone --branch release/79
>>>>                             https://github.com/Ensembl/ensembl.git
>>>>                             ensembl_79
>>>>
>>>>                             PERL5LIB env variable is correctly
>>>>                             pointing to the cloned API:
>>>>
>>>>                             ·echo $PERL5LIB
>>>>                             /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
>>>>
>>>>                             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.
>>>>
>>>>                             I've been reading the docs again and I
>>>>                             can't seen any additional PERL library
>>>>                             requirement.
>>>>
>>>>                             Here's the error log:
>>>>                             http://pastebin.com/VvQrkEQZ
>>>>
>>>>
>>>>                             Thank you!
>>>>
>>>>                             Best regards,
>>>>                             Guille.
>>>>
>>>>
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