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rvosa / bio-phylo

Bio::Phylo - Phyloinformatic analysis using Perl
http://search.cpan.org/dist/Bio-Phylo
GNU General Public License v3.0
16 stars 6 forks source link

unable to reroot trees #30

Closed dbaurain closed 8 years ago

dbaurain commented 8 years ago

Hi Rutger,

I use Bio::Phylo for all my tree parsing and manipulation needs in Perl but one thing: rerooting. Apparently, the corresponding methods (set_root_below and its wrapper reroot) are broken. I did try to fix this myself, but it looks quite complex without fully understanding the way tree are modelled... and frankly, the reason I use your otherwise very nice module is to avoid thinking about that :-) Therefore, what would be your advice to reroot trees (either on leaves or on internal nodes) using Bio::Phylo?

Cheers, Denis

rvosa commented 8 years ago

Hi Denis,

which version are you using? I re-implemented the re-rooting fairly recently because there were, indeed, bugs in earlier versions.

Cheers, Rutger

On Fri, Nov 18, 2016 at 10:59 PM, dbaurain notifications@github.com wrote:

Hi Rutger,

I use Bio::Phylo for all my tree parsing and manipulation needs in Perl but one thing: rerooting. Apparently, the corresponding methods ( set_root_below and its wrapper reroot) are broken. I did try to fix this myself, but it looks quite complex without fully understanding the way tree are modelled... and frankly, the reason I use your otherwise very nice module is to avoid thinking about that :-) Therefore, what would be your advice to reroot trees (either on leaves or on internal nodes) using Bio::Phylo?

Cheers, Denis

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dbaurain commented 8 years ago

Thank you for your fast answer, Rutger. I use the following version:

$ cpanm Bio::Phylo Bio::Phylo is up to date. (0.58)

Cheers, Denis

At Mon, 21 Nov 2016 03:12:59 -0800, notifications@github.com wrote:

Hi Denis,

which version are you using? I re-implemented the re-rooting fairly recently because there were, indeed, bugs in earlier versions.

Cheers, Rutger

On Fri, Nov 18, 2016 at 10:59 PM, dbaurain notifications@github.com wrote:

Hi Rutger,

I use Bio::Phylo for all my tree parsing and manipulation needs in Perl but one thing: rerooting. Apparently, the corresponding methods ( set_root_below and its wrapper reroot) are broken. I did try to fix this myself, but it looks quite complex without fully understanding the way tree are modelled... and frankly, the reason I use your otherwise very nice module is to avoid thinking about that :-) Therefore, what would be your advice to reroot trees (either on leaves or on internal nodes) using Bio::Phylo?

Cheers, Denis

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rvosa commented 8 years ago

Ah, so you installed this from CPAN, correct? I haven't pushed out the new algorithm to CPAN yet. You have two options:

  1. install from the github repository: cpanm git:// github.com/rvosa/bio-phylo.git
  2. replacing the method for set_root_below (in NodeRole.pm) with the one from github: https://github.com/rvosa/bio-phylo/blob/master/lib/Bio/Phylo/Forest/NodeRole.pm#L440-L521

Apologies for the hassle: I should really push out a new release but I haven't got around to it in a while.

dbaurain commented 8 years ago

Thank you, Rutger. That was very helpful!

However, it would be great if you could upload your latest release to CPAN as Bio::Phylo is a dependency of my own modules :-)

Cheers, Denis

At Mon, 21 Nov 2016 08:39:33 -0800, notifications@github.com wrote:

Ah, so you installed this from CPAN, correct? I haven't pushed out the new algorithm to CPAN yet. You have two options:

  1. install from the github repository: cpanm git:// github.com/rvosa/bio-phylo.git
  2. replacing the method for set_root_below (in NodeRole.pm) with the one from github: https://github.com/rvosa/bio-phylo/blob/master/lib/Bio/Phylo/Forest/ NodeRole.pm#L440-L521

Apologies for the hassle: I should really push out a new release but I

haven't got around to it in a while.

You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

rvosa commented 8 years ago

Oh really? Nice to hear, what modules are they?

You're right, though, I do need to do some maintenance. I've also added quite a bit of functionality since the publication so I'm debating if I should write a Bio::Phylo 2.0 manuscript.

On Mon, Nov 21, 2016 at 11:20 PM, dbaurain notifications@github.com wrote:

Thank you, Rutger. That was very helpful!

However, it would be great if you could upload your latest release to CPAN as Bio::Phylo is a dependency of my own modules :-)

Cheers, Denis

At Mon, 21 Nov 2016 08:39:33 -0800, notifications@github.com wrote:

Ah, so you installed this from CPAN, correct? I haven't pushed out the new algorithm to CPAN yet. You have two options:

  1. install from the github repository: cpanm git:// github.com/rvosa/bio-phylo.git
  2. replacing the method for set_root_below (in NodeRole.pm) with the one from github: https://github.com/rvosa/bio-phylo/blob/master/lib/Bio/Phylo/Forest/ NodeRole.pm#L440-L521

Apologies for the hassle: I should really push out a new release but I

haven't got around to it in a while.

You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/rvosa/bio-phylo/issues/30#issuecomment-262085791, or mute the thread https://github.com/notifications/unsubscribe-auth/AAGf-mA5A7DpLIVAUKnjCpjI_MQNGK3Dks5rAhkUgaJpZM4K2-Bi .

dbaurain commented 8 years ago

Yes, but they are not yet publicly released due to still evolving API and incomplete documentation. :-(

Anyway, there is a fairly recent version there: https://bitbucket.org/dbaurain/42/

I think Bio::Phylo is very good. Yet, a few more tutorials and cookbooks would certainly help :-)

Cheers, Denis

At Tue, 22 Nov 2016 10:37:11 -0800, notifications@github.com wrote:

Oh really? Nice to hear, what modules are they?

You're right, though, I do need to do some maintenance. I've also added quite a bit of functionality since the publication so I'm debating if I should write a Bio::Phylo 2.0 manuscript.

On Mon, Nov 21, 2016 at 11:20 PM, dbaurain notifications@github.com wrote:

Thank you, Rutger. That was very helpful!

However, it would be great if you could upload your latest release to CPAN as Bio::Phylo is a dependency of my own modules :-)

Cheers, Denis

At Mon, 21 Nov 2016 08:39:33 -0800, notifications@github.com wrote:

Ah, so you installed this from CPAN, correct? I haven't pushed out the new algorithm to CPAN yet. You have two options:

  1. install from the github repository: cpanm git:// github.com/rvosa/bio-phylo.git
  2. replacing the method for set_root_below (in NodeRole.pm) with the one from github: https://github.com/rvosa/bio-phylo/blob/master/lib/Bio/Phylo/Forest/ NodeRole.pm#L440-L521

Apologies for the hassle: I should really push out a new release but I

haven't got around to it in a while.

You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/rvosa/bio-phylo/issues/30#issuecomment-262085791, or mute the thread https://github.com/notifications/unsubscribe-auth/AAGf- mA5A7DpLIVAUKnjCpjI_MQNGK3Dks5rAhkUgaJpZM4K2-Bi .

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rvosa commented 8 years ago

Ah, cool. If there's anything in particular that you could point out in terms of what is confusing about Bio::Phylo I'd love to hear it. Obviously I have a blind spot. I have gathered from workshops and such that the inheritance tree is not the most intuitive thing in the world when you're looking for docs, anything else that really doesn't make sense?

On Tue, Nov 22, 2016 at 9:45 PM, dbaurain notifications@github.com wrote:

Yes, but they are not yet publicly released due to still evolving API and incomplete documentation. :-(

Anyway, there is a fairly recent version there: https://bitbucket.org/dbaurain/42/

I think Bio::Phylo is very good. Yet, a few more tutorials and cookbooks would certainly help :-)

Cheers, Denis

At Tue, 22 Nov 2016 10:37:11 -0800, notifications@github.com wrote:

Oh really? Nice to hear, what modules are they?

You're right, though, I do need to do some maintenance. I've also added quite a bit of functionality since the publication so I'm debating if I should write a Bio::Phylo 2.0 manuscript.

On Mon, Nov 21, 2016 at 11:20 PM, dbaurain notifications@github.com wrote:

Thank you, Rutger. That was very helpful!

However, it would be great if you could upload your latest release to CPAN as Bio::Phylo is a dependency of my own modules :-)

Cheers, Denis

At Mon, 21 Nov 2016 08:39:33 -0800, notifications@github.com wrote:

Ah, so you installed this from CPAN, correct? I haven't pushed out the new algorithm to CPAN yet. You have two options:

  1. install from the github repository: cpanm git:// github.com/rvosa/bio-phylo.git
  2. replacing the method for set_root_below (in NodeRole.pm) with the one from github: https://github.com/rvosa/bio-phylo/blob/master/lib/Bio/Phylo/Forest/ NodeRole.pm#L440-L521

Apologies for the hassle: I should really push out a new release but I

haven't got around to it in a while.

You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/rvosa/bio-phylo/issues/30#issuecomment-262085791, or mute the thread https://github.com/notifications/unsubscribe-auth/AAGf- mA5A7DpLIVAUKnjCpjI_MQNGK3Dks5rAhkUgaJpZM4K2-Bi .

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