matteocereda / rnamotifs Goto Github PK

Hello,

I'm running into some issues installing GeCo++. Running make on the downloaded source code gives the following errors:

/c4/home/derek/bin/geco++-0.1.464/geco/geco_base.h:347:63: error: ‘memset’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
         if ( value==0 ) memset ( i_mem,0,sizeof ( T ) *length );

Let me know if I can provide more information. I'm very much looking forward to running RNAmotifs on my data.

Thanks,
Derek

Hello Dr,
I try to run RNAmotifs with example data NOVA.txt in "examples" directory.
But at last, I can not result like description as follows:

Selecting significantly enriched motifs...
[1] "NO significant tetrames"

My question is whether the NOVA.txt file did not contain enriched motifs or not?

Hi,
I'm really interested to use RNAmotifs to analyze my differential splicing results however I'm encountering a number of issues with your software when trying to run it on the NOVA example.

Let's first start with the mm9.download.sh script.

• First, the USCS link provided in the 3rd line of the script (i.e. http://hgdownload-test.cse.ucsc.edu/goldenPath/mm9/bigZips/mm9.2bit) is not working

• When replacing this faulty link with a more recent one (i.e. https://hgdownload.soe.ucsc.edu/goldenPath/mm9/bigZips/mm9.2bit), the script is able to download the mm9.2bit file and to convert it to mm9.fasta, as indicated hereafter.

yann.aubert@crct2121-Ubuntu:/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/m3_light/genomes$ ls -lht mm9
total 3,3G
-rwxr-xr-x 1 yann.aubert utilisateurs du domaine 2,6G mars 25 14:56 mm9.fasta
-rwxr-xr-x 1 yann.aubert utilisateurs du domaine 680M juil. 21 2007 mm9.2bit

• I tried running this edited mm9.download.sh script with the original 'python' argument, which threw an error since I only have python3 installed.
• After editing this edited mm9.download.sh script to use python3 instead of the original 'python' argument, I also run into an error. Here is a copy of the script used.

mkdir mm9
cd mm9
##wget http://hgdownload-test.cse.ucsc.edu/goldenPath/mm9/bigZips/mm9.2bit -O mm9.2bit
wget https://hgdownload.soe.ucsc.edu/goldenPath/mm9/bigZips/mm9.2bit -O mm9.2bit

## if not installed downaoload  http://hgdownload.cse.ucsc.edu/admin/exe/twoBitToFa 
../twoBitToFa mm9.2bit mm9.fasta -noMask

cd ../../
printf 'import m3_light\nm3_light.fastasplit("m3_light/genomes/mm9/mm9.fasta")' | python3
mv *.string m3_light/genomes/mm9
rm m3_light/genomes/mm9/mm9.fasta
rm m3_light/genomes/mm9/mm9.2bit

and the copy of the error I ran into.

Résolution de hgdownload.soe.ucsc.edu (hgdownload.soe.ucsc.edu)… 128.114.198.53
Connexion à hgdownload.soe.ucsc.edu (hgdownload.soe.ucsc.edu)|128.114.198.53|:443… connecté.
requête HTTP transmise, en attente de la réponse… 200 OK
Taille : 712923274 (680M)
Enregistre : ‘mm9.2bit’

mm9.2bit 100%[================================================================================================================>] 679,90M 16,3MB/s ds 41s

2024-03-25 14:56:51 (16,6 MB/s) - ‘mm9.2bit’ enregistré [712923274/712923274]

Traceback (most recent call last):
File "", line 1, in
File "/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAMotifs/m3_light/init.py", line 31
print index+1, motif
^^^^^^^^^^^^^^^^^^^^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print(...)?
mv: impossible d'évaluer '*.string': Aucun fichier ou dossier de ce nom
rm: impossible de supprimer 'm3_light/genomes/mm9/mm9.fasta': Aucun fichier ou dossier de ce nom
rm: impossible de supprimer 'm3_light/genomes/mm9/mm9.2bit': Aucun fichier ou dossier de ce nom

As I do not code in Python, I'm having issues sorting out this error.

Regardless of this error I still tried to run RNAmotifs on the NOVA example that is provided using the following code:

#!/bin/bash

cd /mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs

./RNAmotifs.edit.sh /mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs NOVA_regulation NOVA.txt mm9 Mouse 2> /mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/TEST/logs/TEST.log

Here's a copy of RNAmotifs.edit.sh

# Configuration
# --------------------

# Before running this script, please adjust folders (paths) in the r.config and n.config files.

# SET THE ABSOLUTE PATH TO RNAMOTIFS FOLDER
RNAmotifs=$1 # SET THE ABSOLUTE PATH TO RNAMOTIFS FOLDER

cd $RNAmotifs

export PYTHONPATH=$RNAmotifs

# SET THE NAME OF THE RNAMOTIFS RESULTS FOLDER
result_dir=$2

# SET THE ABSOLUTE PATH TO SPLICING CHANGE PATH
splicing_change_infile=$RNAmotifs/TEST/$3

species=$4 # set species

organism=$5 # either "Mouse" or "Human"

p_emp=0.0005

p_fisher=0.1


# Run
# --------------------

N_config="${RNAmotifs}/TEST/${result_dir}.n.config"
R_config="${RNAmotifs}/TEST/${result_dir}.r.config"

# writing gMotifs configuration files

rm $N_config $R_config

if [ ! -f "$N_config" ] ; then
         # if not create the file
         touch "$N_config"
fi

echo "organism=$organism" >> $N_config
echo "splicing_change_file=$splicing_change_infile" >> $N_config
echo "tetramer_folder=$RNAmotifs/tetramers/$result_dir" >> $N_config
echo "results_folder=$RNAmotifs/results/$result_dir" >> $N_config

cp $N_config $R_config

echo "search=N" >> $N_config
echo "search=R" >> $R_config

cat $N_config

cat $R_config

# prepare non-overlapping regions from splicing file

if [ -e m3_light/regions/$result_dir ] ; then
	echo "Dir already present"
else
	mkdir m3_light/regions/$result_dir
fi

python3 m3_light/regions/prepare_regions.py $splicing_change_infile m3_light/regions/$result_dir/overlapping.tab

python3 m3_light/regions/merge_overlapping_regions.py m3_light/regions/$result_dir/overlapping.tab m3_light/regions/$result_dir/$result_dir.tab

rm m3_light/regions/$result_dir/overlapping.tab


# find tetramers in the genome

echo "import m3_light" > tmp.py
echo "m3_light.find_tetramers('${result_dir}', '${species}')" >> tmp.py
python3 tmp.py
rm tmp.py

# move results to tetramers folder

mkdir tetramers
mkdir tetramers/$result_dir
mkdir tetramers/$result_dir/r
mkdir tetramers/$result_dir/nr
cp m3_light/results/$result_dir/motifs.final/pth_0.5/A* tetramers/$result_dir/nr
cp m3_light/results/$result_dir/motifs.final/pth_0.5/C* tetramers/$result_dir/nr
cp m3_light/results/$result_dir/motifs.final/pth_0.5/T* tetramers/$result_dir/nr
cp m3_light/results/$result_dir/motifs.final/pth_0.5/G* tetramers/$result_dir/nr
cp m3_light/results/$result_dir/motifs.final/pth_0.5/W* tetramers/$result_dir/r
cp m3_light/results/$result_dir/motifs.final/pth_0.5/Y* tetramers/$result_dir/r
cp m3_light/results/$result_dir/motifs.final/pth_0.5/S* tetramers/$result_dir/r
cp m3_light/results/$result_dir/motifs.final/pth_0.5/R* tetramers/$result_dir/r


# counting tetramer occurences in the genome

# couting: count the number of exons with tetramer occurrencies in the region of interest r1,r2,r3
# tetramer: calculate the positional specific tetramer occurrences along the RNA splicing map

mkdir results
mkdir results/$result_dir
./gMotifs/build/tetramer -c $N_config
./gMotifs/build/counting -c $N_config
./gMotifs/build/tetramer -c $R_config
./gMotifs/build/counting -c $R_config

# bootstrap and tetramer selection

cd R

Rscript bootstrap-FDR.R ../results $result_dir 10000

Rscript selection_of_tetramers.R ../results $result_dir 10000 $p_fisher $p_emp

Here's a copy of stdout

organism=Mouse
splicing_change_file=/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/TEST/NOVA.txt
tetramer_folder=/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/tetramers/NOVA_regulation
results_folder=/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/results/NOVA_regulation
search=N
organism=Mouse
splicing_change_file=/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/TEST/NOVA.txt
tetramer_folder=/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/tetramers/NOVA_regulation
results_folder=/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/results/NOVA_regulation
search=R
Dir already present

organism=Mouse
Mouse
splicing_change_file=/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/TEST/NOVA.txt
/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/TEST/NOVA.txt
tetramer_folder=/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/tetramers/NOVA_regulation
/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/tetramers/NOVA_regulation
results_folder=/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/results/NOVA_regulation
/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/results/NOVA_regulation
search=N
N
Mouse: 1
Analysis folder: /mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/results/NOVA_regulation/nr/
Search RSYW: N
dIRZ: 0.1
dIRO: 1
inExon: 50
inIntron: 200
Path SP: /mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/TEST/NOVA.txt
Path Tetra: /mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/tetramers/NOVA_regulation/nr/
Array rows: 32874

Motif Length: 0
/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/results/NOVA_regulation/nr/STATS.txt
Impossible open data file: /mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/TEST/NOVA.txt

organism=Mouse
Mouse
splicing_change_file=/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/TEST/NOVA.txt
/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/TEST/NOVA.txt
tetramer_folder=/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/tetramers/NOVA_regulation
/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/tetramers/NOVA_regulation
results_folder=/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/results/NOVA_regulation
/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/results/NOVA_regulation
search=N
N
Mouse: 1
Analysis folder: /mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/results/NOVA_regulation/nr/
Search RSYW: N
dIRZ: 0.1
dIRO: 1
inExon: 50
inIntron: 200
Path SP: /mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/TEST/NOVA.txt
Path Tetra: /mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/tetramers/NOVA_regulation/nr/
Array rows: 32874

Motif Length: 0
/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/tetramers/NOVA_regulation/nr/tetramers_files.txt
Impossible open data file: /mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/TEST/NOVA.txt

organism=Mouse
Mouse
splicing_change_file=/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/TEST/NOVA.txt
/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/TEST/NOVA.txt
tetramer_folder=/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/tetramers/NOVA_regulation
/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/tetramers/NOVA_regulation
results_folder=/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/results/NOVA_regulation
/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/results/NOVA_regulation
search=R
R
Mouse: 1
Analysis folder: /mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/results/NOVA_regulation/r/
Search RSYW: R
dIRZ: 0.1
dIRO: 1
inExon: 50
inIntron: 200
Path SP: /mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/TEST/NOVA.txt
Path Tetra: /mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/tetramers/NOVA_regulation/r/
Array rows: 32874

Motif Length: 0
/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/results/NOVA_regulation/r/STATS.txt
Impossible open data file: /mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/TEST/NOVA.txt

organism=Mouse
Mouse
splicing_change_file=/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/TEST/NOVA.txt
/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/TEST/NOVA.txt
tetramer_folder=/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/tetramers/NOVA_regulation
/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/tetramers/NOVA_regulation
results_folder=/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/results/NOVA_regulation
/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/results/NOVA_regulation
search=R
R
Mouse: 1
Analysis folder: /mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/results/NOVA_regulation/r/
Search RSYW: R
dIRZ: 0.1
dIRO: 1
inExon: 50
inIntron: 200
Path SP: /mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/TEST/NOVA.txt
Path Tetra: /mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/tetramers/NOVA_regulation/r/
Array rows: 32874

Motif Length: 0
/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/tetramers/NOVA_regulation/r/tetramers_files.txt
Impossible open data file: /mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/TEST/NOVA.txt

██████╗ ███╗ ██╗ █████╗ ███╗ ███╗ ██████╗ ████████╗ ██╗ ███████╗ ███████╗
██╔══██╗ ████╗ ██║ ██╔══██╗ ████╗ ████║ ██╔═══██╗ ╚══██╔══╝ ██║ ██╔════╝ ██╔════╝
██████╔╝ ██╔██╗ ██║ ███████║ ██╔████╔██║ ██║ ██║ ██║ ██║ █████╗ ███████╗
██╔══██╗ ██║╚██╗██║ ██╔══██║ ██║╚██╔╝██║ ██║ ██║ ██║ ██║ ██╔══╝ ╚════██║
██║ ██║ ██║ ╚████║ ██║ ██║ ██║ ╚═╝ ██║ ╚██████╔╝ ██║ ██║ ██║ ███████║
╚═╝ ╚═╝ ╚═╝ ╚═══╝ ╚═╝ ╚═╝ ╚═╝ ╚═╝ ╚═════╝ ╚═╝ ╚═╝ ╚═╝ ╚══════╝

Reading tetramer counts....
|======================================================================| 100%
Calculating enrichment....
|======================================================================| 100%
Bootstrapping results....
================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================utilisateur système écoulé
11.008 0.056 11.064
Saving results....

██████╗ ███╗ ██╗ █████╗ ███╗ ███╗ ██████╗ ████████╗ ██╗ ███████╗ ███████╗
██╔══██╗ ████╗ ██║ ██╔══██╗ ████╗ ████║ ██╔═══██╗ ╚══██╔══╝ ██║ ██╔════╝ ██╔════╝
██████╔╝ ██╔██╗ ██║ ███████║ ██╔████╔██║ ██║ ██║ ██║ ██║ █████╗ ███████╗
██╔══██╗ ██║╚██╗██║ ██╔══██║ ██║╚██╔╝██║ ██║ ██║ ██║ ██║ ██╔══╝ ╚════██║
██║ ██║ ██║ ╚████║ ██║ ██║ ██║ ╚═╝ ██║ ╚██████╔╝ ██║ ██║ ██║ ███████║
╚═╝ ╚═╝ ╚═╝ ╚═══╝ ╚═╝ ╚═╝ ╚═╝ ╚═╝ ╚═════╝ ╚═╝ ╚═╝ ╚═╝ ╚══════╝

Selecting significantly enriched motifs...

as well as a copy of stderr:

Traceback (most recent call last):
File "/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/m3_light/regions/merge_overlapping_regions.py", line 87, in
for rid, (chr, strand, list_start, list_stop) in regions.iteritems():
AttributeError: 'dict' object has no attribute 'iteritems'
Traceback (most recent call last):
File "/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/tmp.py", line 1, in
import m3_light
File "/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/m3_light/init.py", line 31
print index+1, motif
^^^^^^^^^^^^^^^^^^^^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print(...)?
mkdir: impossible de créer le répertoire «tetramers»: Le fichier existe
mkdir: impossible de créer le répertoire «tetramers/NOVA_regulation»: Le fichier existe
mkdir: impossible de créer le répertoire «tetramers/NOVA_regulation/r»: Le fichier existe
mkdir: impossible de créer le répertoire «tetramers/NOVA_regulation/nr»: Le fichier existe
cp: impossible d'évaluer 'm3_light/results/NOVA_regulation/motifs.final/pth_0.5/A*': Aucun fichier ou dossier de ce nom
cp: impossible d'évaluer 'm3_light/results/NOVA_regulation/motifs.final/pth_0.5/C*': Aucun fichier ou dossier de ce nom
cp: impossible d'évaluer 'm3_light/results/NOVA_regulation/motifs.final/pth_0.5/T*': Aucun fichier ou dossier de ce nom
cp: impossible d'évaluer 'm3_light/results/NOVA_regulation/motifs.final/pth_0.5/G*': Aucun fichier ou dossier de ce nom
cp: impossible d'évaluer 'm3_light/results/NOVA_regulation/motifs.final/pth_0.5/W*': Aucun fichier ou dossier de ce nom
cp: impossible d'évaluer 'm3_light/results/NOVA_regulation/motifs.final/pth_0.5/Y*': Aucun fichier ou dossier de ce nom
cp: impossible d'évaluer 'm3_light/results/NOVA_regulation/motifs.final/pth_0.5/S*': Aucun fichier ou dossier de ce nom
cp: impossible d'évaluer 'm3_light/results/NOVA_regulation/motifs.final/pth_0.5/R*': Aucun fichier ou dossier de ce nom
mkdir: impossible de créer le répertoire «results»: Le fichier existe
mkdir: impossible de créer le répertoire «results/NOVA_regulation»: Le fichier existe
wc: '/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/tetramers/NOVA_regulation/nr/.bed': Aucun fichier ou dossier de ce nom
wc: '/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/tetramers/NOVA_regulation/nr/.bed': Aucun fichier ou dossier de ce nom
wc: '/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/tetramers/NOVA_regulation/r/.bed': Aucun fichier ou dossier de ce nom
wc: '/mnt/crct-share/CRCT21/Private/Yann/Tools/RNAmotifs/tetramers/NOVA_regulation/r/.bed': Aucun fichier ou dossier de ce nom
Erreur dans strsplit(sapply(strsplit(res[, 1], "/"), function(x) x[length(x)]), :
l'argument n'est pas une chaîne de caractères
Appels : sapply -> lapply -> strsplit
Exécution arrêtée

Not sure if this error has is origin from the faulty mm9.downlaod.sh script or if this is unrelated.

Final point, is there any plans to update RNAmotifs to accomodate more recent mouse and human genome build ? (i.e. GRCm39/mm39; GRCh38) ?

Looking forward for your answer.