[ensembl-dev] VEP 79 API problems
Will McLaren
wm2 at ebi.ac.uk
Fri Jun 5 09:28:01 BST 2015
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> 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 \v and \h escapes that match
> vertical and horizontal whitespace, respectively. \V and \H logically
> match their complements.
>
> \R matches 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] *On
> Behalf Of *Guillermo Marco Puche
> *Sent:* 04 June, 2015 2:10 PM
> *To:* 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
> <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> 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> 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> 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> 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 -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 -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> 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> 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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