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dincarnato / RNAFramework

RNA structure probing and post-transcriptional modifications mapping high-throughput data analysis
http://www.rnaframework.com
GNU General Public License v3.0
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1 folding failed #24

Closed liangyi521 closed 1 year ago

liangyi521 commented 1 year ago

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 1 year ago

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_chrXII465069-466869 and to also replace the "::" and ":" with a "" in the id field of the XML file, and try again?

Thanks. Best, Danny

liangyi521 commented 1 year ago

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 1 year ago

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 1 year ago

Hello Danny,

Attached are my input and output files, and my command is rf-fold -KT NR_132222.1_chrXII_465069-466869.xml

Yiliang

dincarnato commented 1 year ago

I don't see any attachment

dincarnato commented 1 year ago

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 1 year ago

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 1 year ago

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