I am trying to analyze variants in C. elegans genome. I am using genome build WS273. I have all files necessary downloaded (genome sequence, index and gtf feature file).
I tried to run
transvar index --refseq path_to_ws273_feature_file.gtf
this returned:
traceback (most recent call last):
File "/home/nik/Programs/anaconda3/bin/transvar", line 197, in
args.func(args)
File "/home/nik/Programs/anaconda3/lib/python3.6/site-packages/transvar/localdb.py", line 1169, in main_index
db.index([args.refseq])
File "/home/nik/Programs/anaconda3/lib/python3.6/site-packages/transvar/localdb.py", line 335, in index
self.parse_raw(*raw_fns)
File "/home/nik/Programs/anaconda3/lib/python3.6/site-packages/transvar/localdb.py", line 773, in parseraw
info = dict([.split('=') for _ in fields[8].split(';')])
ValueError: dictionary update sequence element #0 has length 1; 2 is required
I have two feature files, gtf and gff3. Both returned the same error message.
Any help would be great.
Thank you!
Good evening,
I am trying to analyze variants in C. elegans genome. I am using genome build WS273. I have all files necessary downloaded (genome sequence, index and gtf feature file).
I tried to run transvar index --refseq path_to_ws273_feature_file.gtf
this returned:
traceback (most recent call last): File "/home/nik/Programs/anaconda3/bin/transvar", line 197, in
args.func(args)
File "/home/nik/Programs/anaconda3/lib/python3.6/site-packages/transvar/localdb.py", line 1169, in main_index
db.index([args.refseq])
File "/home/nik/Programs/anaconda3/lib/python3.6/site-packages/transvar/localdb.py", line 335, in index
self.parse_raw(*raw_fns)
File "/home/nik/Programs/anaconda3/lib/python3.6/site-packages/transvar/localdb.py", line 773, in parseraw
info = dict([.split('=') for _ in fields[8].split(';')])
ValueError: dictionary update sequence element #0 has length 1; 2 is required
I have two feature files, gtf and gff3. Both returned the same error message. Any help would be great. Thank you!