Error in flatfile-to-json.pl

[vpoten]

Running flatfile-to-json with options:
--out
--gff
--trackLabel genes
--key genes
--getSubs
--type gene
--cssclass feature5
--compress
--autocomplete all
--urlTemplate "http://localhost/gene?id={id}&name={name}&strand={strand}&start={start}&end={end}&seq_id={seq_id}"

I get the following error:
Not an ARRAY reference at /home/victor/work_bio/scripts/jbrowse/bin/../lib/../extlib/lib/perl5/Bio/GFF3/LowLevel/Parser/1_0_backcompat.pm line 53.

I will send the gff3 file that causes the error. ¿How?

[vpoten]

I have tested again and maybe the error could be the file size. It fails with 20000 lines but not with a piece of 1000 lines

[rbuels]

Have you tried it again with recent releases of flatfile-to-json.pl? There was a significant memory-usage but that was fixed in 1.3.1.

[vpoten]

Hi,

Yes, I have tried with 1.5.0. The error occurs with a GFF3 file with
500,000 lines (the refGene annotation for homo sapiens)

2012/8/25 Robert Buels notifications@github.com

Have you tried it again with recent releases of flatfile-to-json.pl?
There was a significant memory-usage but that was fixed in 1.3.1.

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Reply to this email directly or view it on GitHubhttps://github.com//issues/109#issuecomment-8027469.

[rbuels]

What version of Bio::GFF3::LowLevel::Parser do you have? To check, you can write this at the command line:

perl -MBio::GFF3::LowLevel::Parser -e 'print $Bio::GFF3::LowLevel::Parser::VERSION,"\n"'

[rbuels]

If it's older than 1.3, you could try upgrading Bio::GFF3::LowLevel::Parser and running it again. An easy way to do this would be to run

bin/cpanm -l extlib Bio::GFF3::LowLevel::Parser

in your jbrowse directory.

[rbuels]

And if an old version of Bio::GFF3::LowLevel isn't the problem, could you provide a link where I can download the file that is giving you this error?

[vpoten]

The Bio::GFF3::LowLevel::Parser version is 1.3

Trying to upgrading it with command bin/cpanm -l extlib
Bio::GFF3::LowLevel::Parser says:
Bio::GFF3::LowLevel::Parser is up to date. (1.3)

The link to the file is:
https://s3.amazonaws.com/gmsAnnot/9606/refGene.gff3.gz

2012/8/28 Robert Buels notifications@github.com

If it's older than 1.3, you could try upgrading
Bio::GFF3::LowLevel::Parser and running it again. An easy way to do this
would be to run

bin/cpanm -l extlib Bio::GFF3::LowLevel::Parser

in your jbrowse directory.

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Reply to this email directly or view it on GitHubhttps://github.com//issues/109#issuecomment-8098445.

[rbuels]

this was a bug in Bio::GFF3::LowLevel::Parser. Fixed in solgenomics/bio-gff3@b1fefd8 and pushed version 1.4 to CPAN.

Please upgrade to Bio::GFF3::LowLevel::Parser version 1.4 once it becomes available on the CPAN mirrors, which might take a few hours.

[vpoten]

After upgrading to 1.4 version of Bio::GFF3::LowLevel::Parser I have
tried flatfile-to-json.pl and it works again.

Thanks,
Best regards
Victor

2012/8/28 Robert Buels notifications@github.com

this was a bug in Bio::GFF3::LowLevel::Parser. Fixed in
solgenomics/bio-gff3@b1fefd8e7c3f27e944a43e78756117b49f284574and pushed version 1.4 to CPAN.

Please upgrade to Bio::GFF3::LowLevel::Parser version 1.4 once it becomes
available on the CPAN mirrors, which might take a few hours.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/109#issuecomment-8104694.