GFF3Loader with allow_whitespace(1) fails to load valid GFF3 with spaces in 9th column

[cjfields]

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Author Name: Nathan Weeks (Nathan Weeks) Original Redmine Issue: 3055, https://redmine.open-bio.org/issues/3055 Original Date: 2010-04-12 Original Assignee: Scott Cain

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When invoked with “allow_whitespace(1)”, the Bio::DB::SeqFeature::Store::GFF3Loader in bioperl-1.6.1 doesn’t handle whitespace in the 9th column.

The following patch seems to fix the issue for our GFF: ################################################################## —- ./Bio/DB/SeqFeature/Store/GFF3Loader.pm.orig 2010-04-12 11:07:34.000000000 –0500 **+ ./Bio/DB/SeqFeature/Store/GFF3Loader.pm 2010-04-12 11:33:13.000000000 –0500 @ -497,7 +497,6@ my @columns = map {$ eq ‘.’ ? undef : $ } split /\t/,$gff_line;

$self->invalid_gff($gff_line) if `columns < 4;

• $self->invalid_gff($gff_line) if `columns > 9 && $allow_whitespace;

{ local $^W = 0; ##################################################################

To save space/time, I’ve neglected to mention the “symptoms” — I can provide this information if requested — but this issue was found by uploading a GFF containing features with the “Target=” attribute into GBrowse 1.70, which sets allow_whitespace(1) for all uploaded GFFs.

[cjfields]

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Original Redmine Comment Author Name: Chris Fields Original Date: 2010-08-03T00:07:09Z

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Nathan, did you bring this up on the gbrowse list? And could you supply an example? I can test this out locally (have both Gbrowse 1.7 and Gbrowse 2.13 running).

[cjfields]

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Original Redmine Comment Author Name: Nathan Weeks Original Date: 2010-08-03T10:15:57Z

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Here’s a single feature with two spaces in the “Target” attribute:

gff-version 3

Gm13 BLASTN match 43640620 43645834 . - . ID=match_sequence501;Target=EST:gi|310573|gb|L20310.1|SOYNOD20A 2728 1

[cjfields]

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Original Redmine Comment Author Name: Jason Stajich Original Date: 2011-03-27T22:08:12Z

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Scott - can you help check this out to see if it is still a bug?