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I am trying to use get_DE_events.py however, I see to run across an issue using it. I have the following created sif:

Sample,Group,Type
Control-01,GROUPA,Control
Control-02,GROUPA,Control
Control-03,GROUPA,Control
EXPERIMENTAL-01,GROUPB,EXPERIMENTAL
EXPERIMENTAL-02,GROUPB,EXPERIMENTAL
EXPERIMENTAL-03,GROUPB,EXPERIMENTAL 

I get the following error (I removed the paths as I am working on an HPC and they require that I do not show paths):

Traceback (most recent call last):
 File /path/to/get_DE_events.py", line 447, in <module>
 call_differential_editing_sites(samples_informations_file) 
 File /path/to/get_DE_events.py", line 132, in call_differential_editing_sites
 edit_level_table = editing_table[all_people]
 File “/path/to/conda/for/EnvironWithPython2.7/pandas/frame.py", line 2934, in __getitem__
 raise_missing=True)
 File “/path/to/conda/for/EnvrionWithPython2.7/pandas/indexing.py", line 1354, in _convert_to_indexer
 return self._get_listlike_indexer(obj, axis, **kwargs)[1]
 File “/path/to/conda/for/EnvironWithPython2.7/pandas/indexing.py", line 1161, in _get_listlike_indexer
 raise_missing=raise_missing)
 File “/path/to/conda/for/EnvironWithPython2.7/pandas/indexing.py", line 1246, in _validate_read_indexer
 key=key, axis=self.obj._get_axis_name(axis)))
KeyError: u"None of [Index([u'Control-01',\n  u'Control-02',\n  u'Control-03',\n  u'EXPERIMENTAL-01',\n  u'EXPERIMENTAL-02',\n  u'EXPERIMENTAL-03'],
\n  dtype='object')] are in the [columns]"

My script is:

python /path/to/get_DE_events.py \
-c 10 \
-cpval 2 \
 -input_file /path/to/sif/file/Control_vs_EXPERIMENTAL.sif \
-f 0.1 \
-mtsA 50.0 \
-mtsB 50.0 \
-sig yes \
-siglevel 0.05 \
-linear

Interestingly a user on Reddit had virtually the same issue found here it seems to be difficult to solve. How would I get around this error.

Hey,
I'm following the published protocol (in Nature) and up to the point 6 in procedure 2 it ran smoothly. It gives errors initially at line 108 (print i, I fixed) but it followed more from line 123. Did somebody else run into these problems?

Thanks.
Ligia

Hi,
Thank you develop this cool tool.
I've completed running REDItoolDnaRna.py on my RNA-seq results, and I want to proceed with differential analysis. However, I'm stuck. Some protocols suggest creating a sample information file and then running the get_DE_events.py program. I tried this but wasn't successful. Others mention using sample_status_file_creator.py to generate the required sample information file (.sif), but I haven't seen this script mentioned in your guidance. Could you please guide me through the correct process? Thank you very much.
Best,
Sixing

Hello,
Could you please confirm that get_de_events.py does not look at potential editing events on the antisense strand? (T->C) . I couldn't find where it considered this in the code, but I could have missed something.
Thank you!
Anu

Dear @tizianoflati @tflati

Thanks for your teams’ efforts! REDItools2 is one of the most popular tools in the study of RNA editing, and I hope to put it into best advantage!
However, I’ve got a little bug when using reditools.py using basic options, and the bug report is as follows:

('[SYSTEM]', 'PYSAM VERSION', '0.17.0') 
 ('[SYSTEM]', 'PYSAM PATH', ['/home/hqy/miniconda3/envs/rna_editing/lib/python2.7/site-packages/pysam'])
Traceback (most recent call last):
File "/mnt/d/BioApp/reditools2.0/src/cineca/reditools.py", line 1374, in <module>
analyze(options)
File "/mnt/d/BioApp/reditools2.0/src/cineca/reditools.py", line 849, in analyze
hostname=socket.gethostbyaddr(netifaces.ifaddresses(interface)[netifaces.AF_INET][0]['addr'])
socket.herror: [Errno 1] Unknown host

It seems that reditools2.0 will try remote connection at the very fist step, but what I need is to run it locally. How can I fix it?

In addition, my environment is as follows:

conda 4.10.3
Python 2.7.15
htslib 1.14
netifaces 0.10.9
openmpi 4.1.2
pip 20.0.2
pysam 0.17.0
psutil 4.4.2
python-socketio 1.8.0
samtools 1.14
sortedcontainers 2.4.0
tabix 1.11

Thanks again for your efforts, and I am sincerely looking forward to your reply and hoping to promote progress in field of RNA editing!

Thanks for developing REDItools2. It’s a nice tool to use. I’ve got some questions about using the tool.

I have 2 groups with 3 replicates in each group. I identified RNA editing events in each sample (replicate) using REDItools2. REDItools2 identified ~300,000 AG editing events in each sample.

Now I want to do differential RNA editing analysis between the 2 groups. I noticed REDItools2 doesn’t provide differential RNA editing analysis. I tried to use the same method for DE analysis (gene) but found there is little overlap of editing events identified among samples. Among ~300,000 AG editing events, there are only ~8000 common editing events among the 6 samples across the 2 groups.

Could you please advise me on how to do differential analysis with the REDItools2 results? Thank you so much.

I am struggling about how to infer strand information with REDItools by using -s parameter for stranded RNA-seq.
For sure by choosing different -s parameter [0/1/2/12] for one sample, the substitutions result will shift.
But among replicate samples, when using the same -s parameter, the nucleotide base in the reference genome and the strand information results came out differently and I don't know why.

Hi,

The genome's contig is too large to use bai format for indexing with samtools, and I can only use csi format. But REDItools seems not compatible with csi when using REDItoolDenovo.py. Is there any solution ?

Best,
Wei

This is mostly an FYI. I ran the 2to3 script that ships with Python on the REDItools source and things seem to work okay after applying the generated patch.

Hi,

I have downloaded REDItools v1.2.1 from https://sourceforge.net/projects/reditools/files/REDItools-1.2.1.zip/download then I tried to run the REDItoolKnown.py and got the following error.

SyntaxError: Non-ASCII character '\xc3' in file /REDItools-1.2.1/reditools/REDItoolKnown.py on line 465, but no encoding declared; see http://python.org/dev/peps/pep-0263/ for details

There seems to be an error in the normByBlat function, line 465 :

else: qual+=squal_[i]-QVALù

Best,

Lara

When I ran REDItools2.0 with parallel_reditools.py, it returned an TyperError, just like blow:

How should I solve it, thank you very.
Additionaly, reditools.py in reditools2.0 could run normally.

Hi,
This is a docker: https://hub.docker.com/layers/claudiologiudice/rna_editing_protocol/latest/images/sha256-70f8ac902f7f9b837530dee3d02c9d22411bfef7dad0d871831cb8e76d9254d3?context=explore. Could you give me a template to run docker by singularity.
And the software already updated: REDItools V2 manual
Note. REDItools V2 is the latest optimized, parallel multi-node version of REDItools.
Important. Reditool_DNA_RNA.py v1.3 available at this link
But, the docker was worked in 2 years ago by claudiologiudice, could you please check the update.
Best,
JG

hey,

I have 3 technical replicates from different library from the same sample. I am using the REDItoolDenovo.py.
Do i need to merge the bam files before analysis or do i need to need to merge the output tables. Please let me know.

Is NPscripts/REDItoolDnaRnav13.py meant to replace main/REDItoolDnaRna.py if using reditools-1.3?

latest fisher package version 0.1.14 (suggested in README) seem can not be installed, pip install finsher==0.1.4 (pip==9.0.1) fixed this

Sorry to bother you. Now I only have single-end RNA seq data. When I runned the REDtools, the strand information always is 2. How can I infer the strand information? Which command I can use?

Hi, I'm running example case using both RNA-seq and DNA-seq.

python /path/to/REDItoolDnaRna.py \
-i  /path/to/rna.bam \
-j  /path/to/dna.bam \
-o  /path/to/my_output \
-f  /path/to/reference.fa

It returned:

Pysam version used: 0.19.0
Script time --> START: 23/06/2022 15:41:38
Analysis ID: 863990752
Analysis on 1 regions.
Started analysis on region: chr21:1-48129895
Job completed for region: chr21:1-48129895
Merging Tables.
Results saved on /gpfs/share/home/2101111835/tools/REDItools-1.2.1/testREDItools/my_output/DnaRna_863990752/outTable_863990752
Script time --> END: 23/06/2022 15:41:43

But I got empty output

(reditools) [2101111835@wm1-login01 ~/tools/REDItools-1.2.1]$cat /path/to/my_output/DnaRna_863990752/outTable_863990752
Region	Position	Reference	Strand	Coverage-q30	MeanQ	BaseCount[A,C,G,T]	AllSubs	Frequency	gCoverage-q30	gMeanQ	gBaseCount[A,C,G,T]	gAllSubs	gFrequency