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Xinglab / rPGA

GNU General Public License v2.0
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Need to add junctions before mapping #2

Closed sstein93 closed 9 years ago

sstein93 commented 9 years ago

In the manual it says to do the mapping and then add the junctions ($rPGA junctions add /path/to/known_splice_junctions) . But, if I try to do the mapping before adding the gtf file I get the error:

Traceback (most recent call last): File "/u/home/s/sstein93/local/bin/rPGA", line 9, in load_entry_point('rPGA==0.0.1', 'console_scripts', 'rPGA')() File "/u/home/s/sstein93/local/lib/python2.7/site-packages/rPGA/scripts/rPGA.py", line 47, in main running.main(sys.argv[2:]) File "/u/home/s/sstein93/local/lib/python2.7/site-packages/rPGA/scripts/running.py", line 490, in main gtf = open(".rPGAJunctions.yaml").readline().rstrip() IOError: [Errno 2] No such file or directory: '.rPGAJunctions.yaml'

bahramis commented 9 years ago

Good catch. In the original structure the user should have entered all the input at the beginning. I changed the structure once I started to put the figure together, forgot to fix the code. Anyways, it's fixed.