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YeoLab / outrigger

Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
http://yeolab.github.io/outrigger/
BSD 3-Clause "New" or "Revised" License
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KeyError: junction #98

Open wbvguo opened 4 years ago

wbvguo commented 4 years ago

Hi ,I try to use outrigger(version 1.1.1, installed using conda) to calculate the PSI value from bam files. But enconter some error, here is the information about the error

Traceback (most recent call last): File "/home/wbguo/apps/anaconda3/envs/outrigger-env/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 2646, in get_loc return self._engine.get_loc(key) File "pandas/_libs/index.pyx", line 111, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1619, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1627, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'junction'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/wbguo/apps/anaconda3/envs/outrigger-env/bin/outrigger", line 11, in load_entry_point('outrigger==1.1.1', 'console_scripts', 'outrigger')() File "/home/wbguo/apps/anaconda3/envs/outrigger-env/lib/python3.7/site-packages/outrigger-1.1.1-py3.7.egg/outrigger/commandline.py", line 1071, in main cl = CommandLine(sys.argv[1:]) File "/home/wbguo/apps/anaconda3/envs/outrigger-env/lib/python3.7/site-packages/outrigger-1.1.1-py3.7.egg/outrigger/commandline.py", line 344, in init self.args.func() File "/home/wbguo/apps/anaconda3/envs/outrigger-env/lib/python3.7/site-packages/outrigger-1.1.1-py3.7.egg/outrigger/commandline.py", line 348, in index index.execute() File "/home/wbguo/apps/anaconda3/envs/outrigger-env/lib/python3.7/site-packages/outrigger-1.1.1-py3.7.egg/outrigger/commandline.py", line 757, in execute event_maker = self.make_graph(junction_exon_triples, db) File "/home/wbguo/apps/anaconda3/envs/outrigger-env/lib/python3.7/site-packages/outrigger-1.1.1-py3.7.egg/outrigger/commandline.py", line 663, in make_graph event_maker = events.EventMaker(junction_exon_triples, db) File "/home/wbguo/apps/anaconda3/envs/outrigger-env/lib/python3.7/site-packages/outrigger-1.1.1-py3.7.egg/outrigger/index/events.py", line 288, in init junction_col].str.split(':').str.get(1) File "/home/wbguo/apps/anaconda3/envs/outrigger-env/lib/python3.7/site-packages/pandas/core/frame.py", line 2800, in getitem indexer = self.columns.get_loc(key) File "/home/wbguo/apps/anaconda3/envs/outrigger-env/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 2648, in get_loc return self._engine.get_loc(self._maybe_cast_indexer(key)) File "pandas/_libs/index.pyx", line 111, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1619, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1627, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'junction'

Do you have any idea how to solve this? Thanks in advance

pengchy commented 4 years ago

The exact same problem was encountered with bam files produced by hisat2.

pilakapa commented 1 year ago

I am also having this problem. I am using sj.out files as input... has anyone found a solution to this problem?