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Magdoll / SQANTI2

SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3
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TypeError on v3.2 #22

Closed kiekyon closed 5 years ago

kiekyon commented 5 years ago

Hi Magdoll,

I ran your updated version of SQANTI2 v3.2 with script below

python ../../../SQANTI2/sqanti_qc2.py \ -t 50 \ test.fasta \ ../../../references/gencode.v31.annotation.gtf.gz \ ../../../references/hg38_noALT.fa

and encountered the following errors -

**** Performing Classification of Isoforms.... Traceback (most recent call last): File "../../../SQANTI2/sqanti_qc2.py", line 1677, in main() File "../../../SQANTI2/sqanti_qc2.py", line 1673, in main run(args) File "../../../SQANTI2/sqanti_qc2.py", line 1325, in run isoforms_info = isoformClassification(args, isoforms_by_chr, refs_1exon_by_chr, refs_exons_by_chr, junctions_by_chr, junctions_by_gene, start_ends_by_gene, genome_dict, indelsJunc, orfDict) File "../../../SQANTI2/sqanti_qc2.py", line 1225, in isoformClassification dist_to_last_junc = rec.junctions[0][1] - orfDict[rec.id].cds_genomic_end TypeError: unsupported operand type(s) for -: 'int' and 'NoneType'

Do you have any suggestions to fix the error? The same command work fine previously on v2.8.

Magdoll commented 5 years ago

I'm aware of this bug...currently working on it. v3.2 added new NMD detection and has been running into several boundaries cases which I'm solving now

Magdoll commented 5 years ago

Hi,

I am aware of this issue and this is becuz of several dependency updates.

Please update to SQANTI2 v3.5 Please update Cupcake to v8.1 Please install gffread and gtfToGenePred using BioConda

conda install -n anaCogent3 -c bioconda ucsc-gtftogenepred openssl=1.0
conda install -n anaCogent3 -c bioconda gffread