[ensembl-dev] VEP 79 API problems
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
Mon Jun 8 16:43:44 BST 2015
Hello Will,
I've currently installed Perl 5.14.4 and seems to be working good. I
also tried 5.22(released a few days) but I had a lot of troubles with
many CPAN modules.
*I only get warnings when using local cache (VEP 79 GrCH38 cache)*.
Cache is indexed cache with convert_cache.pl script.
I'm trying with both example files provided in ensembl-tools and I'm
getting the following warnings:
Argument "-/C" isn't numeric in numeric eq (==) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 5854.
Regards,
Guillermo.
On 08/06/15 10:43, Will McLaren wrote:
> This is probably because Perl can't determine the width of your terminal.
>
> Nothing to worry about, just use --no_progress and just pretend you
> can see animated equals signs moving across your screen :-)
>
> Will
>
> On 5 June 2015 at 13:51, Guillermo Marco Puche
> <guillermo.marco at sistemasgenomicos.com
> <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>
> 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 I got some of my plugins outdated but that's a totally different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
>>> <http://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 <http://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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