Bug #65368 for Bio-NEXUS-Import: BUG: long taxa names are cut in output file

Wed Feb 02 04:55:36 2011 tarajano [...] gmail.com - Ticket created

Subject:	BUG: long taxa names are cut in output file
Date:	Wed, 2 Feb 2011 10:54:54 +0100
To:	bug-Bio-NEXUS-Import [...] rt.cpan.org
From:	manuel alonso <tarajano [...] gmail.com>

Hi Just to report a small bug in (Bio::NEXUS::Import) causing long taxa names ( around 20 and 25 characters) to be cut in the output file. Thanks for taking the time for both developing and giving support to the package Manuel -- "Nothing but heaven itself is better than a friend who is really a friend." Plautus

Wed Feb 02 14:53:34 2011 LIMAONE [...] cpan.org - Correspondence added

Hi Manuel, which format did you try to import? Currently, there is only PHYLIP supported and there the taxa length is hardcoded as 10 characters. But it looks like your format is similar to PHYLIP? So it should be easy to add this functionality... Best, Markus On Wed Feb 02 04:55:36 2011, tarajano@gmail.com wrote: Show quoted text

> Hi > > Just to report a small bug in (Bio::NEXUS::Import) causing long taxa names ( > around 20 and 25 characters) to be cut in the output file. > > Thanks for taking the time for both developing and giving support to the > package > > Manuel > >

Wed Feb 02 14:53:35 2011 The RT System itself - Status changed from 'new' to 'open'

Wed Feb 02 15:13:34 2011 tarajano [...] gmail.com - Correspondence added

Subject:	Re: [rt.cpan.org #65368] BUG: long taxa names are cut in output file
Date:	Wed, 2 Feb 2011 21:12:55 +0100
To:	bug-Bio-NEXUS-Import [...] rt.cpan.org
From:	manuel alonso <tarajano [...] gmail.com>

Hi Markus, I'm trying to import a PHYLIP_DIST_SQUARE format Unfortunately cutting the long taxa names makes several of the taxa names in the matrix to be equal. Thanks a lot for your time Best regards, manuel PHYLIP_DIST_SQUARE format: http://search.cpan.org/~limaone/Bio-NEXUS-Import-0.1.0/lib/Bio/NEXUS/Import.pm#___top On Wed, Feb 2, 2011 at 8:53 PM, LIMAONE via RT < bug-Bio-NEXUS-Import@rt.cpan.org> wrote: Show quoted text

> <URL: https://rt.cpan.org/Ticket/Display.html?id=65368 > > > Hi Manuel, > > which format did you try to import? Currently, there is only PHYLIP > supported and there the > taxa length is hardcoded as 10 characters. But it looks like your format > is similar to PHYLIP? > So it should be easy to add this functionality... > > Best, > Markus > > On Wed Feb 02 04:55:36 2011, tarajano@gmail.com wrote:

> > Hi > > > > Just to report a small bug in (Bio::NEXUS::Import) causing long taxa

> names (

> > around 20 and 25 characters) to be cut in the output file. > > > > Thanks for taking the time for both developing and giving support to the > > package > > > > Manuel > > > >

> > > >

-- "Nothing but heaven itself is better than a friend who is really a friend." Plautus

Wed Feb 02 17:14:03 2011 LIMAONE [...] cpan.org - Correspondence added

I've added a PHYLIP_DIST_SQUARE_BLANK format. This module assumes in this format that the first whitespace (\s) marks the end of the label. So no blanks allowed. Bio::NEXUS::Import should automatically recognize the format. You can get the source code here: https://github.com/lima1/p5-bio-nexus-import (click on "Downloads") Let me know how this works for you! Best, Markus On Wed Feb 02 15:13:34 2011, tarajano@gmail.com wrote: Show quoted text

> Hi Markus, > > I'm trying to import a PHYLIP_DIST_SQUARE format > Unfortunately cutting the long taxa names makes several of the taxa > names in > the matrix to be equal. > > Thanks a lot for your time > > Best regards, > > manuel > > PHYLIP_DIST_SQUARE format: > http://search.cpan.org/~limaone/Bio-NEXUS-Import- > 0.1.0/lib/Bio/NEXUS/Import.pm#___top > > > > > On Wed, Feb 2, 2011 at 8:53 PM, LIMAONE via RT < > bug-Bio-NEXUS-Import@rt.cpan.org> wrote: >

> > <URL: https://rt.cpan.org/Ticket/Display.html?id=65368 > > > > > Hi Manuel, > > > > which format did you try to import? Currently, there is only PHYLIP > > supported and there the > > taxa length is hardcoded as 10 characters. But it looks like your

> format

> > is similar to PHYLIP? > > So it should be easy to add this functionality... > > > > Best, > > Markus > > > > On Wed Feb 02 04:55:36 2011, tarajano@gmail.com wrote:

> > > Hi > > > > > > Just to report a small bug in (Bio::NEXUS::Import) causing long

> taxa

> > names (

> > > around 20 and 25 characters) to be cut in the output file. > > > > > > Thanks for taking the time for both developing and giving support

> to the

> > > package > > > > > > Manuel > > > > > >

> > > > > > > >

> >

Thu Feb 03 06:09:41 2011 tarajano [...] gmail.com - Correspondence added

Subject:	Re: [rt.cpan.org #65368] BUG: long taxa names are cut in output file
Date:	Thu, 3 Feb 2011 12:09:01 +0100
To:	bug-Bio-NEXUS-Import [...] rt.cpan.org
From:	manuel alonso <tarajano [...] gmail.com>

Hi Markus, It worked really fine. However I noticed another situation related to the presence of the character '-' (*minus* character) in the taxa names. If this character is present, 1) the program does not prints out any of the distances related to the corresponding taxas 2) the "*problematic*" taxa names are printed between single quotes ( '* taxaname*' ) in the output file Is it possible for you to implement (allow) *minus* characters in the taxa names? May be "*fixing*" this could be useful to other users. Besides this, everything else is perfectly OK. Best regards and thanks a lot, manuel PS: Of course I could remove them from my input files, but since I'm working with several hundred of files I will have to change it in all of them I don't use (don't plan to) spaces in my taxas' names ;) On Wed, Feb 2, 2011 at 11:14 PM, LIMAONE via RT < bug-Bio-NEXUS-Import@rt.cpan.org> wrote: Show quoted text

> <URL: https://rt.cpan.org/Ticket/Display.html?id=65368 > > > I've added a PHYLIP_DIST_SQUARE_BLANK format. This module assumes in this > format that > the first whitespace (\s) marks the end of the label. So no blanks allowed. > Bio::NEXUS::Import > should automatically recognize the format. You can get the source code > here: > > https://github.com/lima1/p5-bio-nexus-import > > (click on "Downloads") > > Let me know how this works for you! > > Best, > Markus > > On Wed Feb 02 15:13:34 2011, tarajano@gmail.com wrote:

> > Hi Markus, > > > > I'm trying to import a PHYLIP_DIST_SQUARE format > > Unfortunately cutting the long taxa names makes several of the taxa > > names in > > the matrix to be equal. > > > > Thanks a lot for your time > > > > Best regards, > > > > manuel > > > > PHYLIP_DIST_SQUARE format: > > http://search.cpan.org/~limaone/Bio-NEXUS-Import-<http://search.cpan.org/%7Elimaone/Bio-NEXUS-Import-> > > 0.1.0/lib/Bio/NEXUS/Import.pm#___top > > > > > > > > > > On Wed, Feb 2, 2011 at 8:53 PM, LIMAONE via RT < > > bug-Bio-NEXUS-Import@rt.cpan.org> wrote: > >

> > > <URL: https://rt.cpan.org/Ticket/Display.html?id=65368 > > > > > > > Hi Manuel, > > > > > > which format did you try to import? Currently, there is only PHYLIP > > > supported and there the > > > taxa length is hardcoded as 10 characters. But it looks like your

> > format

> > > is similar to PHYLIP? > > > So it should be easy to add this functionality... > > > > > > Best, > > > Markus > > > > > > On Wed Feb 02 04:55:36 2011, tarajano@gmail.com wrote:

> > > > Hi > > > > > > > > Just to report a small bug in (Bio::NEXUS::Import) causing long

> > taxa

> > > names (

> > > > around 20 and 25 characters) to be cut in the output file. > > > > > > > > Thanks for taking the time for both developing and giving support

> > to the

> > > > package > > > > > > > > Manuel > > > > > > > >

> > > > > > > > > > > >

> > > >

-- "Nothing but heaven itself is better than a friend who is really a friend." Plautus

Thu Feb 03 09:15:39 2011 LIMAONE [...] cpan.org - Correspondence added

Strange, seems to be a Bio::NEXUS bug. Anyways, blanks and minus characters are now replaced with underscore. Thanks again for bug report!

Thu Feb 03 09:37:38 2011 tarajano [...] gmail.com - Correspondence added

Subject:	Re: [rt.cpan.org #65368] BUG: long taxa names are cut in output file
Date:	Thu, 3 Feb 2011 15:36:58 +0100
To:	bug-Bio-NEXUS-Import [...] rt.cpan.org
From:	manuel alonso <tarajano [...] gmail.com>

Great!! thanks a lot! Best, manuel On Thu, Feb 3, 2011 at 3:15 PM, LIMAONE via RT < bug-Bio-NEXUS-Import@rt.cpan.org> wrote: Show quoted text

> <URL: https://rt.cpan.org/Ticket/Display.html?id=65368 > > > Strange, seems to be a Bio::NEXUS bug. Anyways, blanks and minus characters > are now replaced > with underscore. Thanks again for bug report! >

-- "Nothing but heaven itself is better than a friend who is really a friend." Plautus

Thu Feb 03 17:39:55 2011 LIMAONE [...] cpan.org - Correspondence added

Should be solved in 0.2.0 Please open a new bug report when you find unparsable files. Thanks again for reporting this.

Thu Feb 03 17:39:56 2011 LIMAONE [...] cpan.org - Status changed from 'open' to 'resolved'

Thu Feb 03 17:42:04 2011 tarajano [...] gmail.com - Correspondence added

Subject:	Re: [rt.cpan.org #65368] BUG: long taxa names are cut in output file
Date:	Thu, 3 Feb 2011 23:41:26 +0100
To:	bug-Bio-NEXUS-Import [...] rt.cpan.org
From:	"manuel a. alonso tarajano" <tarajano [...] gmail.com>

thanks a lot to you manuel On Thu, Feb 3, 2011 at 11:39 PM, LIMAONE via RT < bug-Bio-NEXUS-Import@rt.cpan.org> wrote: Show quoted text

> <URL: https://rt.cpan.org/Ticket/Display.html?id=65368 > > > Should be solved in 0.2.0 Please open a new bug report when you find > unparsable files. Thanks > again for reporting this. >

-- "Nothing but heaven itself is better than a friend who is really a friend." Plautus

Thu Feb 03 17:42:04 2011 The RT System itself - Status changed from 'resolved' to 'open'

Thu Feb 03 18:01:39 2011 LIMAONE [...] cpan.org - Status changed from 'open' to 'resolved'