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ncRNA_gene with child types ncRNA and transcript #189

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gemygk opened this issue Jun 21, 2019 · 2 comments
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ncRNA_gene with child types ncRNA and transcript #189

gemygk opened this issue Jun 21, 2019 · 2 comments
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@cschu @swarbred @lucventurini
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2.0

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@gemygk
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gemygk commented Jun 21, 2019

Hi @lucventurini,

With Mikado version - mikado-20190606_6c8d542, I have lately observed that we have two different ways of defining child features for type 'ncRNA_gene' as shown below.

We only used to have
ncRNA_gene: ncRNA

and not
ncRNA_gene: ncRNA|transcript

File:
/ei/workarea/group-ga/Projects/CB-GENANNO-444_Myzus_persicae_clone_O_v2_annotation/Analysis/mikado-20190606_6c8d542/trans_run1/mikado_all/backup_run/mikado.loci.gff3

scaffold_1      Mikado_loci     ncRNA_gene      8791585 8793523 15      +       .       ID=mikado.scaffold_1G1376;Name=mikado.scaffold_1G1376;multiexonic=False;superlocus=Mikado_superlocus:scaffold_1+:8791585-8872955
scaffold_1      Mikado_loci     transcript      8791585 8793523 15      +       .       ID=mikado.scaffold_1G1376.1;Parent=mikado.scaffold_1G1376;Name=mikado.scaffold_1G1376.1;alias=LIB1777.stringtie_LIB1777_str.1217.1;primary=True

scaffold_1      Mikado_loci     ncRNA_gene      8875936 8876658 15      +       .       ID=mikado.scaffold_1G1390;Name=mikado.scaffold_1G1390;multiexonic=True;superlocus=Mikado_superlocus:scaffold_1+:8875936-8879455
scaffold_1      Mikado_loci     ncRNA   8875936 8876525 14      +       .       ID=mikado.scaffold_1G1390.2;Parent=mikado.scaffold_1G1390;Name=mikado.scaffold_1G1390.2;alias=LIB1777.scallop_sca.gene.LIB1777.1236.12.1;ccode=h;primary=False

This could be a minor thing to fix.

Can you please look into this when you are back.

Thanks,
Gemy
@lucventurini lucventurini added this to the 1.5 milestone Jun 21, 2019
@lucventurini
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On the new run referenced in #186 , I am not seeing any transcript features anywhere. If that is the case at the end of the run, I will close the issue.

@lucventurini
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No transcript feature found in the mikado.loci.gff3 file here:

/ei/workarea/group-ga/Projects/CB-GENANNO-444_Myzus_persicae_clone_O_v2_annotation/Analysis/mikado-20190606_6c8d542/trans_run1/mikado_all/serialise_test_7f87abe

@gemygk , I am closing the issue

lucventurini added a commit that referenced this issue Jul 8, 2019
@lucventurini
Fix #186 and #189 (#191)
9aa33f0 
* Fix #189
* Fix #186
* #183: added static seed from CLI for pick.
* #186: introduced a maximum intron length parameter for mikado prepare (prepare/max_intron_length), with a default value of 1M bps and a minimum value of 20.
* #186: there was a very serious bug in the evaluation of negative truncated ORFs, which potentially led to a lot of them being called incorrectly at the serialisation stage. Refactored the function responsible for the mishap and added a unit-test which confirmed fixing of the bug.
lucventurini added a commit to lucventurini/mikado that referenced this issue Feb 11, 2021
@lucventurini
Fix EI-CoreBioinformatics#186 and EI-CoreBioinformatics#189 (EI-CoreB…
056e2d2 
…ioinformatics#191)

* Fix EI-CoreBioinformatics#189
* Fix EI-CoreBioinformatics#186
* EI-CoreBioinformatics#183: added static seed from CLI for pick.
* EI-CoreBioinformatics#186: introduced a maximum intron length parameter for mikado prepare (prepare/max_intron_length), with a default value of 1M bps and a minimum value of 20.
* EI-CoreBioinformatics#186: there was a very serious bug in the evaluation of negative truncated ORFs, which potentially led to a lot of them being called incorrectly at the serialisation stage. Refactored the function responsible for the mishap and added a unit-test which confirmed fixing of the bug.
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