About AssertionError

[ratschlab]

About AssertionError

[akahles]

Hi @woodydon,
Thank you for reporting the bug. Would you mind sharing your annotation file with me? It looks like SplAdder is hitting some corner case here that I have not thought of and I would like to learn how the error occurs.

[wososa]

Sure, here are some of the lines in the annotation file (Homo_sapiens.GRCh37.75):

chr1 transcribed_unprocessed_pseudogene gene 11869 14412 . + . ID=ENSG00000223972;Name=DDX11L1
chr1 transcribed_unprocessed_pseudogene mRNA 13661 14409 . + . ID=ENST00000518655;Name=DDX11L1;Parent=ENSG00000223972
chr1 transcribed_unprocessed_pseudogene exon 13661 14409 . + . ID=ENST00000518655.4;Name=DDX11L1;Parent=ENST00000518655
chr1 transcribed_unprocessed_pseudogene mRNA 13453 13670 . + . ID=ENST00000450305;Name=DDX11L1;Parent=ENSG00000223972
chr1 transcribed_unprocessed_pseudogene exon 13453 13670 . + . ID=ENST00000450305.6;Name=DDX11L1;Parent=ENST00000450305
chr1 transcribed_unprocessed_pseudogene mRNA 13403 13655 . + . ID=ENST00000518655;Name=DDX11L1;Parent=ENSG00000223972
chr1 transcribed_unprocessed_pseudogene exon 13403 13655 . + . ID=ENST00000518655.3;Name=DDX11L1;Parent=ENST00000518655
chr1 transcribed_unprocessed_pseudogene mRNA 13225 14412 . + . ID=ENST00000515242;Name=DDX11L1;Parent=ENSG00000223972
chr1 transcribed_unprocessed_pseudogene exon 13225 14412 . + . ID=ENST00000515242.3;Name=DDX11L1;Parent=ENST00000515242
chr1 transcribed_unprocessed_pseudogene mRNA 13221 13374 . + . ID=ENST00000450305;Name=DDX11L1;Parent=ENSG00000223972
chr1 transcribed_unprocessed_pseudogene exon 13221 13374 . + . ID=ENST00000450305.5;Name=DDX11L1;Parent=ENST00000450305
chr1 processed_transcript mRNA 13221 14409 . + . ID=ENST00000456328;Name=DDX11L1;Parent=ENSG00000223972
chr1 processed_transcript exon 13221 14409 . + . ID=ENST00000456328.3;Name=DDX11L1;Parent=ENST00000456328
chr1 transcribed_unprocessed_pseudogene mRNA 12613 13052 . + . ID=ENST00000450305;Name=DDX11L1;Parent=ENSG00000223972
chr1 transcribed_unprocessed_pseudogene exon 12613 12697 . + . ID=ENST00000450305.3;Name=DDX11L1;Parent=ENST00000450305
chr1 transcribed_unprocessed_pseudogene exon 12975 13052 . + . ID=ENST00000450305.4;Name=DDX11L1;Parent=ENST00000450305
chr1 transcribed_unprocessed_pseudogene mRNA 12613 12721 . + . ID=ENST00000515242;Name=DDX11L1;Parent=ENSG00000223972
chr1 transcribed_unprocessed_pseudogene exon 12613 12721 . + . ID=ENST00000515242.2;Name=DDX11L1;Parent=ENST00000515242
chr1 processed_transcript mRNA 12613 12721 . + . ID=ENST00000456328;Name=DDX11L1;Parent=ENSG00000223972
chr1 processed_transcript exon 12613 12721 . + . ID=ENST00000456328.2;Name=DDX11L1;Parent=ENST00000456328
chr1 transcribed_unprocessed_pseudogene mRNA 12595 12721 . + . ID=ENST00000518655;Name=DDX11L1;Parent=ENSG00000223972
chr1 transcribed_unprocessed_pseudogene exon 12595 12721 . + . ID=ENST00000518655.2;Name=DDX11L1;Parent=ENST00000518655
chr1 transcribed_unprocessed_pseudogene mRNA 12010 12227 . + . ID=ENST00000450305;Name=DDX11L1;Parent=ENSG00000223972
chr1 transcribed_unprocessed_pseudogene exon 12010 12057 . + . ID=ENST00000450305.1;Name=DDX11L1;Parent=ENST00000450305
chr1 transcribed_unprocessed_pseudogene exon 12179 12227 . + . ID=ENST00000450305.2;Name=DDX11L1;Parent=ENST00000450305
chr1 transcribed_unprocessed_pseudogene mRNA 11874 12227 . + . ID=ENST00000518655;Name=DDX11L1;Parent=ENSG00000223972
chr1 transcribed_unprocessed_pseudogene exon 11874 12227 . + . ID=ENST00000518655.1;Name=DDX11L1;Parent=ENST00000518655
chr1 transcribed_unprocessed_pseudogene mRNA 11872 12227 . + . ID=ENST00000515242;Name=DDX11L1;Parent=ENSG00000223972
chr1 transcribed_unprocessed_pseudogene exon 11872 12227 . + . ID=ENST00000515242.1;Name=DDX11L1;Parent=ENST00000515242

[wososa]

It will be great if you can make gtf as default. I know that gtf file has lots of formats, but you can at least accept the GTF file from Ensemble. It is where I download GTF files.

[akahles]

Thanks for uploading the file. I will look at it shortly. Regarding the GTF request. SplAdder takes either GFF or GTF as input.

[wososa]

Thanks! I just noticed that GTF is also allowed. However, I got the errors...

Parsing annotation from Homo_sapiens.GRCh37.75.sorted.gtf ...
... init structure
Traceback (most recent call last):
File "spladder.py", line 215, in
spladder()
File "spladder.py", line 138, in spladder
(genes, CFG) = init.init_genes_gtf(CFG['anno_fname'], CFG, CFG['anno_fname'] + '.pickle')
File "/Users/admin/Documents/tools/spladder-master/python/modules/init.py", line 64, in init_genes_gtf
genes[tags['gene_id']] = Gene(name=tags['gene_id'], start=start, stop=stop, chr=sl[0], strand=sl[6], source=sl[1], gene_type=tags['gene_type'])
KeyError: 'gene_type

[akahles]

Hm, I see. I'll make the gene_type optional. It is currently not used, anyway.

[wososa]

Looking forward to download the updated version!

[akahles]

I have updated SplAdder to no longer require the gene_type field. Could you re-try and see if GTF parsing works for you now?

Unfortunately, I was not able to reproduce the error above with the GFF file you sent me. I could try again with the full GFF file, if you are willing to send it to me.

[jotrema]

I just got this error. I utilized GRCh38.80.gtf

Traceback (most recent call last):
File "spladder.py", line 255, in
spladder()
File "spladder.py", line 248, in spladder
collect_events(CFG)
File "/home/joel/data/softwares/spladder-master/python/modules/alt_splice/collect.py", line 435, in collect_events
events_all = post_process_event_struct(alt_end_3prime_pos_all, CFG)
File "/home/joel/data/softwares/spladder-master/python/modules/alt_splice/events.py", line 59, in post_process_event_struct
events = make_unique_by_strain(events)
File "/home/joel/data/softwares/spladder-master/python/modules/alt_splice/events.py", line 96, in make_unique_by_strain
assert(event_list[i - 1].gene_name != event_list[i].gene_name)
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()

I hope this helps !

J.

[akahles]

This should be fixed, please re-open if still relevant.