Steffen Möller pushed to branch master at Debian Med / mcaller
Commits: 5116e888 by Steffen Möller at 2020-09-05T22:57:27+02:00 Fixed pickles 2->3 transition (as suggested by Yaroslav) - - - - - 4 changed files: - debian/changelog - + debian/patches/pickl3latin.patch - debian/patches/series - debian/rules Changes: ===================================== debian/changelog ===================================== @@ -2,35 +2,9 @@ mcaller (0.3+git20200621.90f6389-1) UNRELEASED; urgency=medium * Initial release (Closes: #969558) - BLOCKER: - - $ ./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) - moeller@steffen-laptop-debian:~/git/med-team/mcaller/mcaller-0.0$ ./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) + BLOCKER: + - installation should be done properly - needs setup.py ?!? + - .py in executables (secondary) + - README and test files does seem to be in sync with current code. -- Steffen Moeller <[email protected]> Fri, 04 Sep 2020 22:28:05 +0200 ===================================== debian/patches/pickl3latin.patch ===================================== @@ -0,0 +1,13 @@ +Index: mcaller/extract_contexts.py +=================================================================== +--- mcaller.orig/extract_contexts.py ++++ mcaller/extract_contexts.py +@@ -120,7 +120,7 @@ def extract_features(tsv_input,fasta_inp + if not train: + tsv_output = '.'.join(tsv_input.split('.')[:-1])+'.diffs.'+str(k)+'.tmp'+str(startline) + modfi = open(modelfile,'rb') +- model = pickle.load(modfi) ++ model = pickle.load(modfi,encoding="latin1") + modfi.close() + if type(model) != dict: + model = {'general':model} #for compatibility with previously trained model ===================================== debian/patches/series ===================================== @@ -1,2 +1,3 @@ shebang.patch python2to3.patch +pickl3latin.patch ===================================== debian/rules ===================================== @@ -10,5 +10,13 @@ include /usr/share/dpkg/default.mk override_dh_auto_test: ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) + ./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 + ./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 + #./make_bed.py -f testdata/masonread1.eventalign.diffs.6 -d 1 -m 0.5 ./mCaller.py -p testdata/test_positions.txt -r testdata/pb_ecoli_polished_assembly.fasta -e testdata/masonread1.eventalign.tsv -t 4 --train -f testdata/masonread1.fastq endif + +override_dh_auto_clean: + dh_auto_clean + rm -f model_NN_6_m6A.pkl + rm -rf __pycache__ View it on GitLab: https://salsa.debian.org/med-team/mcaller/-/commit/5116e888737a0c7c7e949822a115c456f7a31abd -- View it on GitLab: https://salsa.debian.org/med-team/mcaller/-/commit/5116e888737a0c7c7e949822a115c456f7a31abd You're receiving this email because of your account on salsa.debian.org.
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