jeremymcrae / fitdnm Goto Github PK

Novice (non) Python user with limited departmental support. Apologies in advance.

I'm trying to apply this fitDNM (Python version) to a preliminary dataset of WGS-derived DNMs (100,000 genomes project [UK])

fitDNM cloned and locally installed on CentOS Linux 7; Python 3.7.4

Input:

• standard input with locally imported mutation rates and regional constraint (via gnomAD/ExAC) metrics
• CADD scores are locally hosted, bgzipped and indexed
• provisionally run as an interactive job on a LSF cluster

python scripts/run_fitDNM.py
--males 89
--females 89
--de-novos input/de_novos.tsv
--genome-build GRCh38
--severity PATH_TO_LOCAL_CADD_SNV
--rates PATH_TO_LOCAL_MUT_RATES
--constraint PATH_TO_LOCAL_REGIONAL_CONSTRAINT
--output output/output.txt

Error output:

As shown, recurring issue with "TypeError : [] takes 2 positional arguments but 3 were given"
This error relates to Line 47 but I'm anticipating the same error from lines 53 and 54 on the same logic.

I understand that this can be overcome by addition of self in the definition but am unsure how to overcome this with the list of arguments that are being defined in the function. Apologies again for the naivety. Please let me know if this is more likely to be a local issue which I can try and address.

Any advice would be appreciated regardless. Thanks

(This is more of a question than an issue)

Is there a way to incorporate multiple functional scores (let's say CADD and PolyPhen) other than a single score?
On the separate note, what format would these scores should be if multi columned?