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PacificBiosciences / kineticsTools

Tools for detecting DNA modifications from single molecule, real-time sequencing data
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ipdSummary.py on p4-c2 test data throws Attribute error #5

Closed pb-jlandolin closed 9 years ago

pb-jlandolin commented 9 years ago

I just installed the DNA modification detection tools. But I got the following error when I run the ipdSummary.py using the test data provided by the tool. Could you please let me know how to correctly use it? Thanks.

Best, Lei

python ipdSummary.py --methylFraction --identify m6A,m4C --reference /home/gu/WANG_XIANGYU/Programs/Python/kineticsTools/kineticsTools-master/test/data/lambda/sequence/lambda.fasta /home/gu/WANG_XIANGYU/Programs/Python/kineticsTools/kineticsTools-master/test/data/p4-c2-lambda-mod-decode.cmp.h5

Traceback (most recent call last): File "ipdSummary.py", line 692, in main rcode = kt.start() File "ipdSummary.py", line 342, in start return self.run() File "ipdSummary.py", line 405, in run ret = self._mainLoop() File "ipdSummary.py", line 619, in _mainLoop self.loadReferenceAndModel(self.args.reference, self.args.infile) File "ipdSummary.py", line 531, in loadReferenceAndModel contigs = ReferenceUtils.loadReferenceContigs(referencePath, cmpH5Path) File "/home/gu/lib/python2.7/site-packages/kineticsTools-0.4.0-py2.7-linux-x86_64.egg/kineticsTools/ReferenceUtils.py", line 56, in loadReferenceContigs x.id https://email.tch.harvard.edu/owa/redir.aspx?C=JkcJnDpNckGc3gnKWDwDBIYeuL5xzdEIw6D7zYCLDpyJby76llpXCtIiIIWX-kdBv7K33vAbqe8.&URL=http%3a%2f%2fx.id = None AttributeError: can't set attribute Traceback (most recent call last): File "ipdSummary.py", line 715, in sys.exit(main()) File "ipdSummary.py", line 692, in main rcode = kt.start() File "ipdSummary.py", line 342, in start return self.run() File "ipdSummary.py", line 405, in run ret = self._mainLoop() File "ipdSummary.py", line 619, in _mainLoop self.loadReferenceAndModel(self.args.reference, self.args.infile) File "ipdSummary.py", line 531, in loadReferenceAndModel contigs = ReferenceUtils.loadReferenceContigs(referencePath, cmpH5Path) File "/home/gu/lib/python2.7/site-packages/kineticsTools-0.4.0-py2.7-linux-x86_64.egg/kineticsTools/ReferenceUtils.py", line 56, in loadReferenceContigs x.id https://email.tch.harvard.edu/owa/redir.aspx?C=JkcJnDpNckGc3gnKWDwDBIYeuL5xzdEIw6D7zYCLDpyJby76llpXCtIiIIWX-kdBv7K33vAbqe8.&URL=http%3a%2f%2fx.id = None AttributeError: can't set attribute

dalexander commented 9 years ago

This should be fixed now