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quinlan-lab / pathoscore

pathoscore evaluates variant pathogenicity tools and scores.
MIT License
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code for allowing no annotation with scores #21

Closed jimhavrilla closed 7 years ago

brentp commented 7 years ago

what is the exact error you are getting without this?

jimhavrilla commented 7 years ago

Traceback (most recent call last): File "/uufs/ chpc.utah.edu/common/home/u1021864/software/pathoscore/pathoscore.py", line 471, in annotate(a) File "/uufs/ chpc.utah.edu/common/home/u1021864/software/pathoscore/pathoscore.py", line 373, in annotate scores = [x.split(":") for x in args.scores] TypeError: 'NoneType' object is not iterable

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Tue, Aug 22, 2017 at 4:53 PM, Brent Pedersen notifications@github.com wrote:

what is the exact error you are getting without this?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/quinlan-lab/pathoscore/pull/21#issuecomment-324173690, or mute the thread https://github.com/notifications/unsubscribe-auth/AGQ8BODqzvbhe-ItYUz6SZ8ryXB8SBM8ks5sa1v7gaJpZM4O_Rsr .

jimhavrilla commented 7 years ago

running: python $HOME/software/pathoscore/pathoscore.py annotate benign.combine.vcf.gz --exclude $HOME/software/pathoscore/gene-sets/GRCh37/ad_genes/ad_gene_complement.bed.gz --prefix adgene.benign

and with the changes this works.

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Tue, Aug 22, 2017 at 5:03 PM, Jim Havrilla semjaavria@gmail.com wrote:

Traceback (most recent call last): File "/uufs/chpc.utah.edu/common/home/u1021864/software/ pathoscore/pathoscore.py", line 471, in annotate(a) File "/uufs/chpc.utah.edu/common/home/u1021864/software/ pathoscore/pathoscore.py", line 373, in annotate scores = [x.split(":") for x in args.scores] TypeError: 'NoneType' object is not iterable

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Tue, Aug 22, 2017 at 4:53 PM, Brent Pedersen notifications@github.com wrote:

what is the exact error you are getting without this?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/quinlan-lab/pathoscore/pull/21#issuecomment-324173690, or mute the thread https://github.com/notifications/unsubscribe-auth/AGQ8BODqzvbhe-ItYUz6SZ8ryXB8SBM8ks5sa1v7gaJpZM4O_Rsr .

brentp commented 7 years ago

set default=[] for --scores. that will be a simpler change.

jimhavrilla commented 7 years ago

so change all code back but do that?

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Tue, Aug 22, 2017 at 5:04 PM, Brent Pedersen notifications@github.com wrote:

set default=[] for --scores. that will be a simpler change.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/quinlan-lab/pathoscore/pull/21#issuecomment-324175627, or mute the thread https://github.com/notifications/unsubscribe-auth/AGQ8BF3nQUdo4e4wHgBw1Jw7lMD1RHlqks5sa16bgaJpZM4O_Rsr .

brentp commented 7 years ago

please.

jimhavrilla commented 7 years ago

ok should be good to go now

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Tue, Aug 22, 2017 at 5:06 PM, Brent Pedersen notifications@github.com wrote:

please.

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