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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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plotcircular.py and plotrdbaf.py issue with ROOT #168

Closed gokalpcelik closed 5 years ago

gokalpcelik commented 5 years ago

Hi

I am having an issue with these two plot routines both have very similar problems.

(gatk) sky@GOKALP:/mnt/e/Wes759_CNVnator$ DISPLAY=localhost:0.0 plotcircular.py -chrom $(seq -s "," 1 22)X,Y -bs 1000 -o deneme2.png Wes759_root.root 256 Traceback (most recent call last): File "/mnt/d/scripts/CNVnator/plotcircular.py", line 54, in <module> snp = iof.get_signal(c, bs, "SNP maf",snpflag)[1] File "/mnt/d/scripts/CNVnator/pytools/io.py", line 122, in get_signal n = his.GetSize() AttributeError: 'TObject' object has no attribute 'GetSize' (gatk) sky@GOKALP:/mnt/e/Wes759_CNVnator$

This was tried using different root versions both precompiled and from source however the problem persists. plotbaf.py and regular plotting via view option works fine but these two scrips are failing.

Any comments?

Regards.

gokalpcelik commented 5 years ago

Looks like a bad debug message from python. It is solved.

ilaydabozan commented 4 years ago

Hi, I'm getting the same error;

256 Traceback (most recent call last): File "/home/ilaydab/scratch/CNVnator/plotcircular.py", line 54, in snp = iof.get_signal(c, bs, "SNP maf",snpflag)[1] File "/lustre04/scratch/ilaydab/CNVnator/pytools/io.py", line 121, in getsignal his = self.file.Get("bin" + str(bin_size)).Get(self.signal_name(chr, bin_size, signal, flags)) AttributeError: 'TObject' object has no attribute 'Get'

I am not able to solve it. How did you solve it? Thank you

suvakov commented 4 years ago

Plotcircular tool assumes that root file has precomputed RD and BAF histograms for default bin size 100k for all autosomes. It looks that some of them are missing.

You can create them using "-his 100000" and "-baf 100000" cnvnator step/option.

If you want to use different bin size use plotcircular with option -bs (baf bins - default=100000) and -rdbs (rd bins - default=100000).

saphiecor commented 4 years ago

I created RD and BAF his for 10000 and ran with the option -bs 10000 -rdbs 10000. But I get the same error as the others.

The ratio of mean/sdev where I can get 4 is bin_size 130.

suvakov commented 4 years ago

Can you please list content of root file (./cnvnator -root file.root -ls) and send me (suvakov at gmail) or post here. Thanks.

kalon33 commented 4 years ago

I have the same error:

plotcircular.py -bs 2000 -rdbs 2000 /home/nicolas/cnvnator/mysample.root
256
Traceback (most recent call last):
  File "/usr/bin/plotcircular.py", line 54, in <module>
    snp = iof.get_signal(c, bs, "SNP maf",snpflag)[1]
  File "/usr/lib/python2.7/pytools/io.py", line 122, in get_signal
    n = his.GetSize()
AttributeError: 'TObject' object has no attribute 'GetSize'

I previously ran cnvnator -root /home/nicolas/cnvnator/mysample.root -his 2000 -genome GRCh38 -fasta /home/nicolas/cnvnator/genome_ref.fa (and for other sizes I tested) and cnvnator -root /home/nicolas/cnvnator/mysample.root -baf 2000

$ cnvnator -root /home/nicolas/cnvnator/mysample.root -ls      

Root file: /home/nicolas/cnvnator/mysample.root
-------------------
RD TREES: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT, GL000008.2, GL000009.2, GL000194.1, GL000195.1, GL000205.2, GL000208.1, GL000213.1, GL000214.1, GL000216
.2, GL000218.1, GL000219.1, GL000220.1, GL000221.1, GL000224.1, GL000225.1, GL000226.1, KI270302.1, KI270303.1, KI270304.1, KI270305.1, KI270310.1, KI270311.1, KI270312.1, KI270315.1, KI270316.1, KI27031
7.1, KI270320.1, KI270322.1, KI270329.1, KI270330.1, KI270333.1, KI270334.1, KI270335.1, KI270336.1, KI270337.1, KI270338.1, KI270340.1, KI270362.1, KI270363.1, KI270364.1, KI270366.1, KI270371.1, KI2703
72.1, KI270373.1, KI270374.1, KI270375.1, KI270376.1, KI270378.1, KI270379.1, KI270381.1, KI270382.1, KI270383.1, KI270384.1, KI270385.1, KI270386.1, KI270387.1, KI270388.1, KI270389.1, KI270390.1, KI270
391.1, KI270392.1, KI270393.1, KI270394.1, KI270395.1, KI270396.1, KI270411.1, KI270412.1, KI270414.1, KI270417.1, KI270418.1, KI270419.1, KI270420.1, KI270422.1, KI270423.1, KI270424.1, KI270425.1, KI27
0429.1, KI270435.1, KI270438.1, KI270442.1, KI270448.1, KI270465.1, KI270466.1, KI270467.1, KI270468.1, KI270507.1, KI270508.1, KI270509.1, KI270510.1, KI270511.1, KI270512.1, KI270515.1, KI270516.1, KI2
70517.1, KI270518.1, KI270519.1, KI270521.1, KI270522.1, KI270528.1, KI270529.1, KI270530.1, KI270538.1, KI270539.1, KI270544.1, KI270548.1, KI270579.1, KI270580.1, KI270581.1, KI270582.1, KI270583.1, KI
270584.1, KI270587.1, KI270588.1, KI270589.1, KI270590.1, KI270591.1, KI270593.1, KI270706.1, KI270707.1, KI270708.1, KI270709.1, KI270710.1, KI270711.1, KI270712.1, KI270713.1, KI270714.1, KI270715.1, K
I270716.1, KI270717.1, KI270718.1, KI270719.1, KI270720.1, KI270721.1, KI270722.1, KI270723.1, KI270724.1, KI270725.1, KI270726.1, KI270727.1, KI270728.1, KI270729.1, KI270730.1, KI270731.1, KI270732.1, 
KI270733.1, KI270734.1, KI270735.1, KI270736.1, KI270737.1, KI270738.1, KI270739.1, KI270740.1, KI270741.1, KI270742.1, KI270743.1, KI270744.1, KI270745.1, KI270746.1, KI270747.1, KI270748.1, KI270749.1,
 KI270750.1, KI270751.1, KI270752.1, KI270753.1, KI270754.1, KI270755.1, KI270756.1, KI270757.1

DIRECTORIES FOR BIN SIZES: 5000, 300, 500, 1000, 2000, 3000, 4000

@suvakov any idea for a cause for this problem?