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Type Error when segway identify task generates layered output #25

Closed EricR86 closed 10 years ago

EricR86 commented 10 years ago

From epa...@uw.edu on August 27, 2012 19:09:35

Traceback (most recent call last): File "/net/noble/vol1/home/epaul9/arch/Linux/RHEL6/x86_64/bin/segway", line 8, in load_entry_point('segway==1.2.0.dev- r9225 ', 'console_scripts', 'segway')() File "/net/noble/vol1/home/epaul9/arch/Linux/RHEL6/x86_64/lib/python2.7/segway-1.2.0.dev_r9225-py2.7.egg/segway/run.py", line 2483, in main return runner() File "/net/noble/vol1/home/epaul9/arch/Linux/RHEL6/x86_64/lib/python2.7/segway-1.2.0.dev_r9225-py2.7.egg/segway/run.py", line 2312, in call self.run(_args, *_kwargs) File "/net/noble/vol1/home/epaul9/arch/Linux/RHEL6/x86_64/lib/python2.7/segway-1.2.0.dev_r9225-py2.7.egg/segway/run.py", line 2303, in run self.run_identify_posterior() File "/net/noble/vol1/home/epaul9/arch/Linux/RHEL6/x86_64/lib/python2.7/segway-1.2.0.dev_r9225-py2.7.egg/segway/run.py", line 2225, in run_identify_posterior IdentifySaver(self)(world) File "/net/noble/vol1/home/epaul9/arch/Linux/RHEL6/x86_64/lib/python2.7/segway-1.2.0.dev_r9225-py2.7.egg/segway/output.py", line 139, in call bigbed_outfilename=self.make_filename(self.bigbed_filename, world)) File "/net/noble/vol1/home/epaul9/arch/Linux/RHEL6/x86_64/lib/python2.7/segway-1.2.0.dev_r9225-py2.7.egg/segway/layer.py", line 355, in layer segmentation.save(outfilename, bigbed_outfilename) File "/net/noble/vol1/home/epaul9/arch/Linux/RHEL6/x86_64/lib/python2.7/segway-1.2.0.dev_r9225-py2.7.egg/segway/layer.py", line 252, in save ends = self.write(outfile) File "/net/noble/vol1/home/epaul9/arch/Linux/RHEL6/x86_64/lib/python2.7/segway-1.2.0.dev_r9225-py2.7.egg/segway/layer.py", line 287, in write self.write_trackline(outfile) File "/net/noble/vol1/home/epaul9/arch/Linux/RHEL6/x86_64/lib/python2.7/segway-1.2.0.dev_r9225-py2.7.egg/segway/layer.py", line 278, in write_trackline print >>final_outfile, " ".join(self.trackline) TypeError

Original issue: http://code.google.com/p/segway-genome/issues/detail?id=25

EricR86 commented 10 years ago

From epa...@uw.edu on October 18, 2012 17:04:10

In layer.py on line 234

self.trackline = update_trackline(self.trackline, updates)

should be

update_trackline(self.trackline, updates)

because update_trackline mutates its arguments and returns None.

EricR86 commented 10 years ago

From epa...@cs.washington.edu on March 25, 2013 13:39:23

Status: Fixed