[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I got some of my plugins outdated but that's a totally different and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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