padidehdanaee / bprna Goto Github PK

Hi, I recently had to run bpRNA.pl multiple times on the same set of files. However, I observed a strange behavior for the following file of chain A of PDB entry 6e8s obtained from the test data of https://doi.org/10.1093/bioinformatics/btab165:

# 6e8s_A
1       G       38
2       C       37
3       U       36
4       A       35
5       C       34
6       G       33
7       A       32
8       A       0
9       G       0
10      G       0
11      A       0
12      A       0
13      G       0
14      G       0
15      A       22
16      U       0
17      U       0
18      G       0
19      G       0
20      U       27
21      A       28
22      U       15
23      G       0
24      U       0
25      G       0
26      G       0
27      U       20
28      A       21
29      U       0
30      A       0
31      U       0
32      U       7
33      C       6
34      G       5
35      U       4
36      A       3
37      G       2
38      C       1

The produced structures in the .st file differ from time to time:

(((((((.......[....{(]....})...)))))))
(((((((.......[....({]....)}...)))))))

I fixed this behavior by sorting the connected components before running the for loop in line ~1085.
From my point of view, this behavior is problematic e.g. when generating datasets for Pk predictions that have to be reproducible and if this is the intended behavior of bpRNA, please let me know.

Thanks and best regards.

Folder Load_bpRNA_1m_Perl .zip has a space in the name noticed it when trying to unizp in Bash.

There are many statements here where the values contain apostrophes without being escaped or enclosed in double quotation marks, which may cause issues.
Such like:

Long-term feature request: Make it possible for others to easily contribute new data to the bpRNA-1m database. Perhaps use dolthub.com to keep each cell of data in all those database tables under git-like version-control:
https://www.dolthub.com/blog/2020-10-07-merge-on-the-web/#roadmap
The dolt clone create a local copy of the database (similar to git clone): https://docs.dolthub.com/introduction/quickstart

I was hoping to do a pull request to add some tiny bits of data, like some missing rnacentral links. But I see no easy way to do it currently: seems like I would need to unzip those huge zip files, make changes, then re-zip, right?

Hi, trying to run the perl script on a .dbn file, and came across the following error:

hugokitano@Hugos-MacBook-Pro bpRNA % perl bpRNA.pl bpRNA_CRW_1.dbn
Can't locate Graph.pm in @INC (you may need to install the Graph module) (@INC contains: /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-thread-multi-2level /Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.4 /System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18 /System/Library/Perl/Extras/5.18/darwin-thread-multi-2level /System/Library/Perl/Extras/5.18 .) at bpRNA.pl line 2.
BEGIN failed--compilation aborted at bpRNA.pl line 2.

What should I do? Thank you!