##sequence-region Scaffold6154 1 10437 - 0-base issue about apollo

[nathandunn]

gff is 1-based coordinates - but the problem is probably the same sort of thing as before given the GBOL that follows the gff - it'd take looking at it properly to see what's going on as updating the start to either 1 or 2 results in stops in the coding sequence:

##sequence-region Scaffold6154 1 10437
Scaffold6154 WebApollo gene 0 7739 . + . Name=A464CB0E837997D1C1D87DDEDDB8E0BB;date_creation=2014-07-2;owner=[email protected];ID=A464CB0E837997D1C1D87DDEDDB8E0BB;date_last_modified=2014-07-2
Scaffold6154 WebApollo mRNA 0 7739 . + . Name=Scaffold6154:75-606;date_creation=2014-07-2;Parent=A464CB0E837997D1C1D87DDEDDB8E0BB;owner=[email protected];ID=CC2EB7C7C3624151D93F1A98191540FA;date_last_modified=2014-07-2
Scaffold6154 WebApollo exon 0 726 . + . Name=3D2A22D0A9059B01D465618B00B659BB;date_creation=2014-07-2;Parent=CC2EB7C7C3624151D93F1A98191540FA;owner=[email protected];ID=3D2A22D0A9059B01D465618B00B659BB;date_last_modified=2014-07-2
Scaffold6154 WebApollo CDS 2 726 . + 0 Name=CC2EB7C7C3624151D93F1A98191540FA-CDS;date_creation=2014-07-2;Parent=CC2EB7C7C3624151D93F1A98191540FA;owner=[email protected];ID=CC2EB7C7C3624151D93F1A98191540FA-CDS;Note=Manually set translation start;date_last_modified=2014-07-2
Scaffold6154 WebApollo CDS 7449 7725 . + 2 Name=CC2EB7C7C3624151D93F1A98191540FA-CDS;date_creation=2014-07-2;Parent=CC2EB7C7C3624151D93F1A98191540FA;owner=[email protected];ID=CC2EB7C7C3624151D93F1A98191540FA-CDS;Note=Manually set translation start;date_last_modified=2014-07-2
Scaffold6154 WebApollo exon 7449 7739 . + . Name=81268E97CF1F24E9DC7053C58897FB0D;date_creation=2014-07-2;Parent=CC2EB7C7C3624151D93F1A98191540FA;owner=[email protected];ID=81268E97CF1F24E9DC7053C58897FB0D;date_last_modified=2014-07-2

typename : gene, type : sequence:gene - chado uniquename : A464CB0E837997D1C1D87DDEDDB8E0BB : -1 - 7739
typename : mRNA - chado uniquename : CC2EB7C7C3624151D93F1A98191540FA : -1 - 7739
typename : exon - chado uniquename : 3D2A22D0A9059B01D465618B00B659BB : -1 - 726
typename : CDS - chado uniquename : CC2EB7C7C3624151D93F1A98191540FA-CDS : 1 - 7725
typename : exon - chado uniquename : 81268E97CF1F24E9DC7053C58897FB0D : 7448 - 7739

[nathandunn]

Need to verify / fix.

[monicacecilia]

I need more background to test this.
And here is a refresher: https://www.biostars.org/p/84686/

[cmdcolin]

While it's unclear how the original problem was generated, I have tried to simulate inputs that might cause problems like this. In one case, I used my script test_add_feature.pl to generate inputs where fmin/fmax are larger than UINT_MAX (other thread #33 (comment))

For example this command that i mentioned in that thread still has problems with Apollo2

perl client/apollo/tests/perl_tests/test_add_feature.pl --username [email protected] --password demo --url http://localhost:8080/apollo --featuredata '[{"location":{"fmin":4294967296,"fmax": 559153,"strand":1},"type":{"cv":{"name":"sequence"},"name":"mRNA"},"name":"TEST4","children":[{"location":{"fmin":559153,"fmax": 559153,"strand":1},"type":{"cv":{"name":"sequence"},"name":"exon"}}]}]' --track Group1.1

This will return a "valid" feature with invalid coordinates (the gff3 results will actually say the start position is -1, not 0)

[nathandunn]

@cmdcolin K . . thanks I'll take a look.

[nathandunn]

We won't encounter reference sequences scaffolds larger than an int value.