[med-svn] [Git][med-team/mcaller][master] Fixed pickles 2->3 transition (as suggested by Yaroslav)

[Steffen Möller]

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 at 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 <moeller at debian.org>  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
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