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mkado util convert - additional gene lines #384

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swarbred opened this issue Mar 3, 2021 · 4 comments · Fixed by #383
Closed

mkado util convert - additional gene lines #384

swarbred opened this issue Mar 3, 2021 · 4 comments · Fixed by #383
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@lucventurini
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@swarbred
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swarbred commented Mar 3, 2021

run with the test file (part of the minos input test set)

reat_xspecies_wport_wex_wutr.loci.regionA.gtf (this is from reat homology so a mikado output file)

This has a gene (mikado.Chr3G297) with two transcripts they are not found adjacent in the file and this results in mikado convert generating an additional gene line (invalid)

[swarbred@EI-HPC interactive Models]$ mikado util convert -if gtf -of gff3 reat_xspecies_wport_wex_wutr.loci.regionA.gtf reat_xspecies_wport_wex_wutr.loci.regionA.gff3
[swarbred@EI-HPC interactive Models]$ grep mikado.Chr3G297 reat_xspecies_wport_wex_wutr.loci.regionA.gff3
Chr3	Mikado_xspecies_loci	gene	1123361	1140723	.	+	.	ID=mikado.Chr3G297
Chr3	Mikado_xspecies_loci	mRNA	1123361	1140723	31.36	+	.	ID=mikado.Chr3G297.2;Parent=mikado.Chr3G297;Name=mikado.Chr3G297.2;alias=Ppersica_Prupe.8G212600.1.v2.1.m1;avg_ef1=27;avg_jf1=33;canonical_junctions=1,2,3;canonical_number=3;canonical_proportion=1;ccode=j;cds_ccode=j;cds_exon_f1=33;cds_id=46;cds_junction_f1=50;has_start_codon=True;has_stop_codon=True;is_reference=True;max_ef1=100;max_jf1=100;min_ef1=0;min_jf1=0;multiexonic=True;note=Prupe.8G212600.1.v2.1|cov:100.00|id:59.30|cds_id:46.38|cds_exon_f1:33.33|cds_junction_f1:50.00|cds_ccode:j|min_ef1:0.00|max_ef1:100.00|avg_ef1:27.50|min_jf1:0.00|max_jf1:100.00|avg_jf1:33.33|xscore:10.00;primary=False;retained_intron=False;superlocus=Mikado_xspecies_superlocus:Chr3+:1123361-1140723;xscore=10
Chr3	Mikado_xspecies_loci	CDS	1123361	1123379	.	+	0	ID=mikado.Chr3G297.2.CDS1;Parent=mikado.Chr3G297.2
Chr3	Mikado_xspecies_loci	exon	1123361	1123379	.	+	.	ID=mikado.Chr3G297.2.exon1;Parent=mikado.Chr3G297.2
Chr3	Mikado_xspecies_loci	CDS	1124237	1124367	.	+	2	ID=mikado.Chr3G297.2.CDS2;Parent=mikado.Chr3G297.2
Chr3	Mikado_xspecies_loci	exon	1124237	1124367	.	+	.	ID=mikado.Chr3G297.2.exon2;Parent=mikado.Chr3G297.2
Chr3	Mikado_xspecies_loci	CDS	1124995	1125035	.	+	0	ID=mikado.Chr3G297.2.CDS3;Parent=mikado.Chr3G297.2
Chr3	Mikado_xspecies_loci	exon	1124995	1125035	.	+	.	ID=mikado.Chr3G297.2.exon3;Parent=mikado.Chr3G297.2
Chr3	Mikado_xspecies_loci	CDS	1140504	1140723	.	+	1	ID=mikado.Chr3G297.2.CDS4;Parent=mikado.Chr3G297.2
Chr3	Mikado_xspecies_loci	exon	1140504	1140723	.	+	.	ID=mikado.Chr3G297.2.exon4;Parent=mikado.Chr3G297.2
Chr3	Mikado_xspecies_loci	gene	1140318	1140723	.	+	.	ID=mikado.Chr3G297
Chr3	Mikado_xspecies_loci	mRNA	1140318	1140723	43.03	+	.	ID=mikado.Chr3G297.1;Parent=mikado.Chr3G297;Name=mikado.Chr3G297.1;alias=Crubella_Carub.0003s0351.1.v1.1.m1;avg_ef1=72;avg_jf1=73;canonical_junctions=1;canonical_number=1;canonical_proportion=1;cds_exon_f1=100;cds_id=96;cds_junction_f1=100;has_start_codon=True;has_stop_codon=True;is_reference=True;max_ef1=100;max_jf1=100;min_ef1=0;min_jf1=0;multiexonic=True;note=carub.0003s0351.1.v1.1|cov:100.00|id:96.90|cds_id:96.91|cds_exon_f1:100.00|cds_junction_f1:100.00|cds_ccode:=|min_ef1:0.00|max_ef1:100.00|avg_ef1:72.50|min_jf1:0.00|max_jf1:100.00|avg_jf1:73.33|xscore:70.00;primary=True;superlocus=Mikado_xspecies_superlocus:Chr3+:1123361-1140723;xscore=70
Chr3	Mikado_xspecies_loci	CDS	1140318	1140388	.	+	0	ID=mikado.Chr3G297.1.CDS1;Parent=mikado.Chr3G297.1
Chr3	Mikado_xspecies_loci	exon	1140318	1140388	.	+	.	ID=mikado.Chr3G297.1.exon1;Parent=mikado.Chr3G297.1
Chr3	Mikado_xspecies_loci	CDS	1140504	1140723	.	+	1	ID=mikado.Chr3G297.1.CDS2;Parent=mikado.Chr3G297.1
Chr3	Mikado_xspecies_loci	exon	1140504	1140723	.	+	.	ID=mikado.Chr3G297.1.exon2;Parent=mikado.Chr3G297.1
@lucventurini
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This is due to the fact the mikado util convert presumes that the file is already sorted .. I can amend this but the memory requirements will go up.

I will probably add a flag, like -as, --assume-sorted to avoid putting things in memory.

@swarbred
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swarbred commented Mar 3, 2021

The file is coordinate sorted (as gffread) but not sorted by each gene (i.e as gt gff --sort). Yes the -as option seems useful

@lucventurini
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Coordinate sorted as in transcript lines might come after exon lines? My parsers won't particularly like that, but I can see what to do ..

lucventurini added a commit that referenced this issue Mar 3, 2021
@lucventurini
Fix #384
4a05df5
@lucventurini lucventurini self-assigned this Mar 3, 2021
@lucventurini
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lucventurini commented Mar 3, 2021 •
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Hi @swarbred

b071298 will fix this. It can also deal with files sorted purely by chrom, start, end.

Best,

lucventurini added a commit that referenced this issue Mar 3, 2021
@lucventurini
Fix 4a05df5 (for #384)
b071298
@lucventurini lucventurini linked a pull request Mar 13, 2021 that will close this issue
Fix v2.1.2 #383
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lucventurini added a commit that referenced this issue Mar 15, 2021
@lucventurini
Fix v2.1.2 (#383)
469b1c7 
# Version 2.2.0
Removed Cython from the requirements.txt file. This allows to perform the tests correctly in a Conda environment (as Conda disallows installing Cython as part of a distributed package).
As a result of this change, the preferred installation procedure from source has to be slightly amended:
- either install using `pip wheel -w dist . && pip install dist/Mikado*whl`
- or install with `python setup.py bdist_wheel` **after** having forcibly installed Cython, with `pip install Cython` or the like.

Other changes:
- Fix [#381](#381): now Mikado will be able to guess correctly 
  the input file format, instead of relying on the file name extension or user's settings. Sniffing for files 
  provided as a stream is *disabled* though.
- Fix [#382](#382): now Mikado can accept generic BED12 files 
  as input junctions, not just Portcullis junctions. This allows e.g. a user to provide a ***set of gene models*** 
  in BED12 format as sources of valid junctions.
- Fix [#384](#384): now Mikado convert deals properly with 
  unsorted GTFs/GFFs. 
- Fix [#386](#386): dealing better with unsorted GFFs/GTFs for 
  the stats utility.
- Fix [#387](#387): now Mikado will always use a static seed, 
  rather than generating a new one per call unless specifically instructed to do so. The old behaviour can still be 
  replicated by either setting the `seed` parameter to `null` (ie `None`) in the configuration file, or by 
  specifying `--random-seed` during the command invocation.
- General increase in code unit-test coverage; in particular:  
  - Slightly increased the unit-test coverage for the locus classes, e.g. properly covering the `as_dict` and `load_dict`
    methods. Minor bugfixes related to the introduction of these unit-tests.
- `Mikado.parsers.to_gff` has been renamed to `Mikado.parsers.parser_factory`.
- The code related to the transcript padding has been moved to the submodule `Mikado.transcripts.pad`, rather than 
  being part of the `Mikado.loci.locus` submodule.
- Mikado will error informatively if the scoring configuration file is malformed.
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Fix v2.1.2 EI-CoreBioinformatics/mikado
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