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Oshlack / ALLSorts

ALLSorts is a B-Cell Acute Lymphoblastic Leukemia (B-ALL) subtype classifier. From gene expression counts to over 18 subtypes.
MIT License
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IndexError: index 0 is out of bounds for axis 0 with size 0 #4

Closed hanxuelian closed 4 years ago

hanxuelian commented 4 years ago

ALLSorts can run successfully with test data, but an error is reported with my own test data. The details are as follows.

1)inputfile(reads count on each gene) ,hezhiyan,LIANGXIAOLAN,LIAOJIFENG,lilingyi,LXINZHE,NGR200625001,qianli,qinpeixiang,luozhimin,luoyangying,huangzhegnhan,chenziyang,zhuxiangyan,zhaojinsheng,qinzuofa,huanglianbin,xuxunjia,xuyongyi,ZYZ DSC3,0,0,0,0,4,1,1,0,0,0,7,7,0,0,0,0,0,1,0 IGF2BP1,1,0,0,0,37,0,0,0,0,0,1,4,0,0,0,0,0,0,0 KCNK3,0,0,9,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0 IGJ,0,9,0,0,0,10,0,88,1,8,7,2,0,4,0,0,0,0,0 PTPRM,0,0,12,14,1,1,1,1,0,4,4,8,3,0,1,0,0,0,0 KCNN1,0,0,0,1,23,0,1,1,2,23,5,70,0,1,0,0,2,5,0 CD99,8,0,0,0,9,125,0,109,504,301,979,86,486,88,219,267,5,6,2 HAP1,0,1,0,0,13,5,0,1,1,4,4,1,0,0,0,0,0,0,2 AGAP1,0,0,13,16,1,1,1,8,0,11,79,0,0,0,0,0,0,1,1 CHST2,1,6,207,85,1,9,10,177,0,30,9,14,2,47,25,4,0,7,0 SLC2A5,0,0,0,0,0,35,0,5,48,28,230,22,114,60,26,6,2,0,0 IFITM1,0,1,2,0,0,13,5,203,168,310,75,52,97,9,145,24,4,12,0 ABHD3,0,2,0,1,13,2,0,7,1,10,22,28,5,2,2,3,2,3,5 PCLO,2,6,1,0,23,1,4,0,8,7,16,70,1,0,0,0,0,7,2 TNS1,0,0,0,0,0,13,0,408,29,55,158,9,10,10,3,4,0,1,1 NCF2,5,0,2,4,8,21,4,83,44,200,89,26,17,21,177,25,9,14,4 MIB1,0,0,0,4,1,12,0,20,20,3,84,26,7,2,4,5,0,2,0 TCFL5,6,1,11,26,6,18,3,26,78,27,288,291,94,27,50,28,0,0,0 ARHGEF4,7,10,108,2,3,0,2,8,0,10,1,16,1,1,0,1,0,4,6 RGMA,0,0,0,0,4,0,1,10,0,4,1,3,2,0,0,0,0,0,0

2)command line python ALLSorts -samples gene.forRF.classifier.HTseqCount.xls -destination test/

3)Error

Prediction Mode

Loading classifier... Saving predictions... Traceback (most recent call last): File "/home/hanxl/Software/anaconda3/envs/allsorts/lib/python3.8/runpy.py", line 194, in _run_module_as_main return _run_code(code, main_globals, None, File "/home/hanxl/Software/anaconda3/envs/allsorts/lib/python3.8/runpy.py", line 87, in _run_code exec(code, run_globals) File "ALLSorts/main.py", line 20, in allsorts.run() File "ALLSorts/allsorts.py", line 90, in run probabilities = allsorts_clf.predict_proba(ui.samples, parents=ui.parents) File "ALLSorts/pipeline.py", line 115, in predict_proba Xt = transform.transform(Xt) File "ALLSorts/stages/preprocessing.py", line 108, in transform counts = self.normalise.transformMor(counts.transpose()).transpose() File "/home/hanxl/TEST/ExpressionProfile/LIMINGZE/ph-like_method/AllSorts/tools/MoRP/morp/morp.py", line 122, in transformMor counts_normalised, success = self._applyMor(counts, step_3_logs, self.gm) File "/home/hanxl/TEST/ExpressionProfile/LIMINGZE/ph-like_method/AllSorts/tools/MoRP/morp/morp.py", line 102, in _applyMor gene_check = step_3_logs.index[0] File "/home/hanxl/Software/anaconda3/envs/allsorts/lib/python3.8/site-packages/pandas/core/indexes/base.py", line 3929, in getitem return getitem(key) IndexError: index 0 is out of bounds for axis 0 with size 0

breons commented 3 years ago

MoRP is no longer used in ALLSorts for future reference.