update Graph interface for module compat

[ggraham]

Graph::Undirected->new to Graph->new(undirected=>1)

[porteusconf]

Do we also need a PR to tweak first few lines of bpRNA.pl something like this?

#!/usr/bin/env  perl -w
use Graph;
use Graph::Undirected;
use strict;

I verified that use Graph::Undirected; is not needed if bpRNA.pl has the 2 PR tweaks. My knowledge of perl is zero, so I'm not sure which is the best way to solve the method new error, which is also seen in

$ perl drawSegmentGraphs.pl  bpRNA_RFAM_34891.bpseq 
Can't locate object method "new" via package "Graph::Undirected" (perhaps you forgot to load "Graph::Undirected"?) at drawSegmentGraphs.pl line 996, <BPS> line 192.

Whatever fix is chosen, it should be applied also to drawSegmentGraphs.pl as well.
See padidehdanaee#2 (comment)

Also, need to document format of *.st (structure type) files. And/or at least add info in help that:

• PKBP means "Pseudo-knot Base Pair"
• NCBP means "Noncanonical Base Pair"

[EthanHolleman]

Just wanted to drop by to say @porteusconf adding use Graph::Undirected; fixed the issues with bpRNA.pl I was having. Without it would get error message below.

Can't locate object method "new" via package "Graph::Undirected" (perhaps you forgot to load "Graph::Undirected"?)

My perl knowledge is basically non-existent but wanted to bump this for visibility.

[hendrixlab]

Hi everyone, I have added

use Graph::Undirected
to the latest version. I think it is really cool that there is a discussion happening here, I missed it until now. I think I also found that this update was needed on my end. I also fixed a couple other things. It should now take directly the output of RNAfold when saved to a file, such as:

cat sequence.fasta | RNAfold > result.dbn

so that you can run this directly with something like:

perl bpRNA.pl result.dbn

At some point, I would like to fix things so that bpRNA.pl can take input piped in.

[porteusconf]

At some point, I would like to fix things so that bpRNA.pl can take input piped in.

Maybe add new Issue "Fix things so that bpRNA.pl can take input piped in."

Other random thoughts...

I think it is really cool that there is a discussion happening here, I missed it until now.

Maybe enable github-issues and/or github-discussions to track such postings?

Are github-issues disabled for this project? Perhaps consider enabling them to make feedback and discussion easier. In any case, for me, even when logged into github, I don't see any icons to click for Issues nor Discussions. Or if I manually go to https://github.com/hendrixlab/bpRNA/issues it redirects to pulls here: https://github.com/hendrixlab/bpRNA/pulls

I understand that many github repos disable issues because if you start to see lots of issues it can become overwhelming and unwieldly. But I don't think you'll see too many issues: the original site, not updated since 2018, has had only 5 issues total https://github.com/padidehdanaee/bpRNA/issues?q=is%3Aopen

Consider deleting fork dependency to abandoned /padidehdanaee/bpRNA

The hendrixlab/bpRNA seems to be only active fork:
https://techgaun.github.io/active-forks/index.html#padidehdanaee/bpRNA
Since issues and PR posted at /padidehdanaee/bpRNA have gone unanswered for years now, make reasonable effort to contact padidehdanaee and propose hendrixlab take over. One way is:
https://stackoverflow.com/questions/16052477/delete-fork-dependency-of-a-github-repository

To help others find your github repo, maybe add an issue titled "Is this project abandoned or dead or no longer supported?" to /padidehdanaee/bpRNA with a suggestion to use /hendrixlab/bpRNA instead.

We might even want to copy over all the unresolved issues from /padidehdanaee/bpRNA to hendrixlab/bpRNA since /hendrixlab/bpRNA seems to be where we want to do work now.