Hello, I had a look at mCaller and made a few shorts a bringing it to Python3. The 2nd test-invocation of the README.md is just fine, the first one however is a bit less forgiving. I first thought this is a ByteIO vs StringIO error but I have not touched anything like it, but if folks know some magic out there - would be nice.
The source tree just made it to https://salsa.debian.org/med-team/mcaller . Many thanks Steffen $ ./mCaller.py -p testdata/test_positions_A.txt -r testdata/pb_ecoli_polished_assembly.fasta -e testdata/masonread1.eventalign.tsv -d r95_twobase_model_NN_6_m6A.pkl -f testdata/masonread1.fastq testdata/ 1 contigs 1 threads Traceback (most recent call last): File "./mCaller.py", line 188, in <module> main() File "./mCaller.py", line 184, in main distribute_threads(args.positions,args.motif,args.tsv,read2qual,args.reference,num_refs,base,mod,args.threads,args.num_variables, File "./mCaller.py", line 59, in distribute_threads extract_features(tsvname,refname,read2qual,nvariables,skip_thresh,qual_thresh,modelfile,classifier,0,endline=bytesize,train=train,pos_label=training_pos_dict,base=base,motif=motif,positions_list=positions_list) File "/home/moeller/git/med-team/mcaller/mcaller-0.0/extract_contexts.py", line 123, in extract_features model = pickle.load(modfi) UnicodeDecodeError: 'ascii' codec can't decode byte 0xb9 in position 1: ordinal not in range(128) $ ./mCaller.py -p testdata/test_positions_m6A.txt -r testdata/pb_ecoli_polished_assembly.fasta -e testdata/masonread1.eventalign.tsv -d r95_twobase_model _NN_6_m6A.pkl -f testdata/masonread1.fastq testdata/ 1 contigs 1 threads Traceback (most recent call last): File "./mCaller.py", line 188, in <module> main() File "./mCaller.py", line 184, in main distribute_threads(args.positions,args.motif,args.tsv,read2qual,args.reference,num_refs,base,mod,args.threads,args.num_variables, File "./mCaller.py", line 59, in distribute_threads extract_features(tsvname,refname,read2qual,nvariables,skip_thresh,qual_thresh,modelfile,classifier,0,endline=bytesize,train=train,pos_label=training_pos_dict,base=base,motif=motif,positions_list=positions_list) File "/home/moeller/git/med-team/mcaller/mcaller-0.0/extract_contexts.py", line 123, in extract_features model = pickle.load(modfi) UnicodeDecodeError: 'ascii' codec can't decode byte 0xb9 in position 1: ordinal not in range(128)
