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gtf issue with talon_initialize_database #157

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dl870 opened this issue Nov 20, 2024 · 0 comments
Open

gtf issue with talon_initialize_database #157

dl870 opened this issue Nov 20, 2024 · 0 comments

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@dl870
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dl870 commented Nov 20, 2024

Hi, I am having an issue with talon_initialize_database after reformatting my gtf - sr_reformatted.txt
I get the following error when running : talon_initialize_database --f sr_reformatted.gft --a Sr18 --g WsBPS18 --o sr_flf1

bulk update genes...
bulk update gene_annotations...
Traceback (most recent call last):
File "/home/dl870/.conda/envs/longread-tools/bin/talon_initialize_database", line 8, in
sys.exit(main())
File "/home/dl870/.conda/envs/longread-tools/lib/python3.7/site-packages/talon/initialize_talon_database.py", line 1073, in main
populate_db(db_name, annot_name, chrom_genes, chrom_transcripts, exons, genome_build)
File "/home/dl870/.conda/envs/longread-tools/lib/python3.7/site-packages/talon/initialize_talon_database.py", line 634, in populate_db
add_transcripts(c, transcripts, annot_name, gene_id_map, genome_build)
File "/home/dl870/.conda/envs/longread-tools/lib/python3.7/site-packages/talon/initialize_talon_database.py", line 743, in add_transcripts
db_gene_id = gene_id_map[native_gene_id]
KeyError: 'None'

I don't know if its the GTF file error or not? I tried running it without reformatting and it ran but then talon couldn't find the annotations later.

Cheers!

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