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XiaoTaoWang / NeoLoopFinder

A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
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Fail on correct-cnv #8

Closed wzhang42 closed 2 years ago

wzhang42 commented 2 years ago

Hi, XiaoTao, I continuously use the following command lines for calculate-cnv, segment-cnv and correct-cnv. 1.) calculate-cnv -g hg19 -H hic_SH-SY5Y.inter_5000.cool --output ./calculate-cnv.txt -e MboI --cachefolder ./neoloopfinder 2.) segment-cnv --cnv-file ./calculate-cnv.txt --binsize 5000 --output ./segmented_cnv.txt --nproc 12 3.) correct-cnv -H hic_SH-SY5Y.inter_5000.cool --cnv-file ./segmented_cnv.txt --nproc 12 --logFile cnv-norm.log

The first two, calculate-cnv, and segment-cnv are ok. But correct-cnv throw the following Error message. Could you give me any clues or suggestions to fix it. Thank you in advance. .... root INFO @ 07/22/21 20:42:28:

ARGUMENT LIST:

Cooler URI = hic_SH-SY5Y.inter_5000.cool

CNV Profile = ./segmented_cnv.txt

Number of Processes = 12

Log file name = cnv-norm.log

root INFO @ 07/22/21 20:42:38: Match CNV segmentation to matrix bins Traceback (most recent call last): File "/home/wzhang42/.conda/envs/neoloop/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 3080, in get_loc return self._engine.get_loc(casted_key) File "pandas/_libs/index.pyx", line 70, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 101, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 4554, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 4562, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'weight'

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

Traceback (most recent call last): File "/home/wzhang42/.conda/envs/neoloop/bin/correct-cnv", line 92, in run bincnv.assign_cnv(args.hic) File "/home/wzhang42/.conda/envs/neoloop/lib/python3.7/site-packages/neoloop/cnv/loadcnv.py", line 87, in assign_cnv bias = cooler_lib.bins().fetch(ref_k)['weight'].values File "/home/wzhang42/.conda/envs/neoloop/lib/python3.7/site-packages/pandas/core/frame.py", line 3024, in getitem indexer = self.columns.get_loc(key) File "/home/wzhang42/.conda/envs/neoloop/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 3082, in get_loc raise KeyError(key) from err KeyError: 'weight'

XiaoTaoWang commented 2 years ago

Ah, the error occurred because the current version assumes there is a column "weight" in the bin table of the input cool file, which stores the bias vector from the standard ICE normalization. To avoid the error, just run "cooler balance" on your cool file.

wzhang42 commented 2 years ago

This works. Thank you so much