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zhpn1024 / ribotish

Ribo-seq TIS Hunter, predicting translation initiation sites and ORFs using riboseq data
http://dx.doi.org/10.1038/s41467-017-01981-8
GNU General Public License v3.0
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ribotish tisdiff error?ZeroDivisionError: integer division or modulo by zero #16

Open etmorefish opened 3 years ago

etmorefish commented 3 years ago

hi,when I use the ribotish tisdiff ,some error information as follows: my command : ribotish tisdiff -1 pred1.txt -2 pred2.txt -a v1.sort.bam -b vi2.sort.bam -g test.gtf -o diff -v error informations:

Loading 2 TIS data... 1 TISs in pred1.txt. 1 TISs in pred2.txt. 1 TISs in total. Reading bams... JN Estimate scale factor... Traceback (most recent call last): File "/usr/bin/ribotish", line 4, in import('pkg_resources').run_script('ribotish==0.2.6', 'ribotish') File "/usr/lib/python2.7/site-packages/pkg_resources/init.py", line 654, in run_script self.require(requires)[0].run_script(script_name, ns) File "/usr/lib/python2.7/site-packages/pkg_resources/init.py", line 1441, in run_script exec(script_code, namespace, namespace) File "/usr/lib/python2.7/site-packages/ribotish-0.2.6-py2.7.egg/EGG-INFO/scripts/ribotish", line 56, in

File "/usr/lib/python2.7/site-packages/ribotish-0.2.6-py2.7.egg/EGG-INFO/scripts/ribotish", line 34, in main

File "build/bdist.linux-x86_64/egg/ribotish/run/tisdiff.py", line 254, in run File "build/bdist.linux-x86_64/egg/ribotish/zbio/exp.py", line 207, in TMM ZeroDivisionError: integer division or modulo by zero

etmorefish commented 3 years ago

the files pred1.txt , pred2.txt , v1.sort.bam , vi2.sort.bam are in the same fold ?

zhpn1024 commented 3 years ago

1 TISs in pred1.txt. 1 TISs in pred2.txt. 1 TISs in total.

Why there is only one TIS?

zhpn1024 commented 3 years ago

The error is because the number of TISs are too small, and result in fail of normalization.

etmorefish commented 3 years ago

image hi,using this tool how to get the picture ?

etmorefish commented 3 years ago

the number of TISs is more than 100.How many at least ?

zhpn1024 commented 3 years ago

The log showed only one TIS selected. Do you use the full transcript annotation? The figure is generated in another script. I'll update later.

shwdmsh commented 3 years ago

Why there is only one TIS? @zhpn1024 The genome is virus. There is some error?

zhpn1024 commented 3 years ago

There are filters to select significant TISs (--ipth --iqth).

zhpn1024 commented 3 years ago

It is difficult to open github these days.

shwdmsh commented 3 years ago

@zhpn1024 thanks .I will try these parameters.