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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.
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’
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:
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
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
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
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
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.
The text was updated successfully, but these errors were encountered:
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.
and the copy of the error I ran into.
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:
Here's a copy of RNAmotifs.edit.sh
Here's a copy of stdout
as well as a copy of stderr:
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.
The text was updated successfully, but these errors were encountered: