dincarnato/RNAFramework

1 folding failed

liangyi521 opened this issue · 8 comments

liangyi521 commented

Dear Danny,
When working with my yeast data, the tools were pretty smooth, up until the rf-fold step. Whether I enter the separate xml file or the combine xml file, the result is failure.

rf-fold yeast_dms_1_norm/NR_132222.1::chrXII:465069-466869.xml
[+] Checking method's requirements...
[+] Making output directory tree...
[+] Importing XML file(s) [1 imported]
[+] Folding RNA structures [Last: none]
[+] Folding statistics:

[] Folded transcripts: 0
[] Discarded transcripts: 1 total
0 XML parsing failed
0 constraint file generation failed
0 FASTA file generation failed
1 folding failed
0 I/O error

[+] All done.

Best,
yiliang

dincarnato commented

Hello Yiliang,

I have a hunch that the presence of colon chars in the transcript name/id (those "::" and ":") might drive Vienna RNAfold crazy.
Can you please try to rename the file to NR_132222.1_chrXII_465069-466869 and to also replace the "::" and ":" with a "_" in the id field of the XML file, and try again?

Thanks.
Best,
Danny

liangyi521 commented

Dear Danny,

Thank you for your reply, I replaced "::" for "_", as shown below, still failed.

rf-fold NR_132222.1_chrXII_465069-466869.xml

[+] Checking method's requirements...
[+] Making output directory tree...
[+] Importing XML file(s) [1 imported]
[+] Folding RNA structures [Last: none]
[+] Folding statistics:

[] Folded transcripts: 0
[] Discarded transcripts: 1 total
0 XML parsing failed
0 constraint file generation failed
0 FASTA file generation failed
1 folding failed
0 I/O error

Best,
yiliang

dincarnato commented

Please show the command you are executing. Also, try to rerun the same command adding the -KT parameter and share the content of the output folder.

Danny

liangyi521 commented
dincarnato commented

I don't see any attachment

dincarnato commented

I see you still have one of the “:” in the id field in the XML file.
Can you please try with the amended XML file?

dincarnato commented

I tried by removing the ":" you missed, and the file works fine for me.
I will add a check to remove invalid characters that might make RNAfold crash in the next release.
Please let me know if i can close the issue.

Danny

liangyi521 commented

Great! After I removed all the ":", the file works fine.
It would be nice to get it fixed in the next version.
Thank you again.

Yiliang