Error running pyjacker

[pandurang-kolekar]

Hi @e-sollier ,

I was running pyjacker by providing example myeloid enhancers file along with TPM matrix and SV breakpoints in hg19. However I ran into the following KeyError. I tried adding/removing 'chr' prefix but it still failed. Please help resolve this issue. Thanks!

multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/research_jude/rgs01_jude/groups/xmagrp/projects/AMLRelapse/xmagrp/CohortTracker/dev/pyjacker/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/research_jude/rgs01_jude/groups/xmagrp/projects/AMLRelapse/xmagrp/CohortTracker/dev/pyjacker/lib/python3.9/site-packages/pyjacker/pyjacker.py", line 325, in find_EH_gene
d["enhancers"],d["super_enhancers"],enhancer_score = find_enhancers_orientation(data["breakpoints"],data["TADs"],data["df_enhancers"],sample,gene)
File "/research_jude/rgs01_jude/groups/xmagrp/projects/AMLRelapse/xmagrp/CohortTracker/dev/pyjacker/lib/python3.9/site-packages/pyjacker/breakpoints.py", line 167, in find_enhancers_orientation
for bp in breakpoints[chr]:
KeyError: '14'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/research_jude/rgs01_jude/groups/xmagrp/projects/AMLRelapse/xmagrp/CohortTracker/dev/pyjacker/bin/pyjacker", line 7, in
sys.exit(main())
File "/research_jude/rgs01_jude/groups/xmagrp/projects/AMLRelapse/xmagrp/CohortTracker/dev/pyjacker/lib/python3.9/site-packages/pyjacker/pyjacker.py", line 393, in main
null_distribution = pyjack.estimate_null_distribution()
File "/research_jude/rgs01_jude/groups/xmagrp/projects/AMLRelapse/xmagrp/CohortTracker/dev/pyjacker/lib/python3.9/site-packages/pyjacker/pyjacker.py", line 281, in estimate_null_distribution
df_result = self.find_EH(random_candidates=True)
File "/research_jude/rgs01_jude/groups/xmagrp/projects/AMLRelapse/xmagrp/CohortTracker/dev/pyjacker/lib/python3.9/site-packages/pyjacker/pyjacker.py", line 218, in find_EH
results = list(tqdm(pool.imap(find_EH_gene,self.gene_list),total=len(self.gene_list),disable=random_candidates,file=sys.stdout))
File "/research_jude/rgs01_jude/groups/xmagrp/projects/AMLRelapse/xmagrp/CohortTracker/dev/pyjacker/lib/python3.9/site-packages/tqdm/std.py", line 1169, in iter
for obj in iterable:
File "/research_jude/rgs01_jude/groups/xmagrp/projects/AMLRelapse/xmagrp/CohortTracker/dev/pyjacker/lib/python3.9/multiprocessing/pool.py", line 870, in next
raise value
KeyError: '14'

[e-sollier]

Hello, sorry about this bug. I've just created a new version 1.1.6 which should fix the issue. Let me know if you encounter other issues!

[pandurang-kolekar]

Thanks @e-sollier, I made a small change to return statement in the commit e7624ac
and it's working as expected.

[e-sollier]

Yes indeed there was a small mistake in my fix, it's now properly fixed in v1.1.7.