ALoFT: Annotation of Loss-of-Function Transcripts: Installation

Question

[Shicheng Guo]

Hi All,

Who has successfully installed this software?

http://aloft.gersteinlab.org/

ALoFT provides extensive annotations to putative loss-of-function variants (LoF) in protein-coding genes including functional, evolutionary and network features. Further, ALoFT can predict the impact of premature stop variants and classify them as dominant disease-causing, recessive disease-causing and benign variants.

I installed the software according to the http://aloft.gersteinlab.org/ and then:

 cd /gpfs/home/guosa/hpc/tools/aloft/aloft-annotate
./aloft

However, the app always reports error:

 File "./aloft", line 1028
    outdata = {i : "" for i in set(basicparams) | set(LOFparams) | set(spliceparams)}
                        ^
SyntaxError: invalid syntax

Thanks

sudo apt install python-autopep8
autopep8 -i aloft

usage: ./aloft [-h] [--version] [--vcf VCF] [--vat VAT] [--output OUTPUT]
               [--cache CACHE] [--nmd_threshold NMD_THRESHOLD] [--verbose]
               [--data DATA]

Run ALoFT predictions. You must provide a VCF or VAT file as input. See
options below.