search

YeoLab / outrigger

Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
http://yeolab.github.io/outrigger/
BSD 3-Clause "New" or "Revised" License
61 stars 22 forks source link

NotImplementedError: "flankBed" #93

Open YutingMa68 opened 4 years ago

YutingMa68 commented 4 years ago

Hi,when I used the outrigger software to do the variable splicing analysis, I got the following error. I haven't found a solution. I have to ask you. Can you help me find a solution? NotImplementedError: "flankBed" does not appear to be installed or on the path, so this method is disabled. Please install a more recent version of BEDTools and re-import to use this method. my python is python3.5

I have reinstalled the software and it has not solved this problem.

File "outrigger", line 6, in sys.exit(outrigger.commandline.main()) File "commandline.py", line 1071, in main cl = CommandLine(sys.argv[1:]) File "/hwfssz1/ST_MCHRI/DISEASE/USER/liuhankui/bin/software/conda/envs/outrigger-env/lib/python3.5/site-packages/outrigger/commandline.py", line 344, in init self.args.func() File "/hwfssz1/ST_MCHRI/DISEASE/USER/liuhankui/bin/software/conda/envs/outrigger-env/lib/python3.5/site-packages/outrigger/commandline.py", line 352, in validate validate.execute() File "/hwfssz1/ST_MCHRI/DISEASE/USER/liuhankui/bin/software/conda/envs/outrigger-env/lib/python3.5/site-packages/outrigger/commandline.py", line 834, in execute exonA, exonB, splice_abbrev) File "/hwfssz1/ST_MCHRI/DISEASE/USER/liuhankui/bin/software/conda/envs/outrigger-env/lib/python3.5/site-packages/outrigger/commandline.py", line 787, in exon_pair_splice_sites exonA, splice_abbrev, 'downstream') File "/hwfssz1/ST_MCHRI/DISEASE/USER/liuhankui/bin/software/conda/envs/outrigger-env/lib/python3.5/site-packages/outrigger/commandline.py", line 800, in individual_exon_splice_sites exon_bed, self.genome, self.fasta, direction) File "/hwfssz1/ST_MCHRI/DISEASE/USER/liuhankui/bin/software/conda/envs/outrigger-env/lib/python3.5/site-packages/outrigger/validate/check_splice_sites.py", line 57, in read_splice_sites flanked = bed.flank(l=left, r=right, s=True, genome=genome) File "/hwfssz1/ST_MCHRI/DISEASE/USER/liuhankui/bin/software/conda/envs/outrigger-env/lib/python3.5/site-packages/pybedtools/bedtool.py", line 806, in decorated result = method(self, *args, **kwargs) File "/hwfssz1/ST_MCHRI/DISEASE/USER/liuhankui/bin/software/conda/envs/outrigger-env/lib/python3.5/site-packages/pybedtools/bedtool.py", line 204, in not_implemented_func raise NotImplementedError(help_str) NotImplementedError"flankBed" does not appear to be installed or on the path, so this method is disabled. Please install a more recent version of BEDTools and re-import to use this method.