mCaller - Unicode error - anybody who has encountered this before/having an instant idea?

[Steffen Möller <steffen_moeller@gmx.de>]

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)