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Id: 122733
Status: resolved
Priority: 0/
Queue: bioperl-run

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Owner: Nobody in particular
Requestors: Richard.Francis [...] telethonkids.org.au
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Subject: Bio::Tools::Run::Alignment::Muscle profile line 320
Date: Mon, 7 Aug 2017 07:33:34 +0000
To: "bug-bioperl-run [...] rt.cpan.org" <bug-bioperl-run [...] rt.cpan.org>
From: Richard Francis <Richard.Francis [...] telethonkids.org.au>
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Dear all, On line 320 in Bio::Tools::Run::Alignment::Muscle is a throw() that prevents versions of muscle other than v3.52 from being run with this module. The error "profile does not work for this version of muscle” is returned. I looks like this was added to avoid segfaults in profile-profile alignments in early v3.6 releases of Muscle. The software is at v3.8.31 at the moment. I am not doing profile-profile alignments in my work and so cannot check to see if this aspect of muscle is stable but if the developers of muscle have resolved these issues then it would be great if this throw() could be removed to allow newer versions of muscle to be used with this module. Kind regards, Richard
Subject: Re: [rt.cpan.org #122733] AutoReply: Bio::Tools::Run::Alignment::Muscle profile line 320
Date: Mon, 7 Aug 2017 08:11:27 +0000
To: "bug-bioperl-run [...] rt.cpan.org" <bug-bioperl-run [...] rt.cpan.org>
From: Richard Francis <Richard.Francis [...] telethonkids.org.au>
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Dear all, I just filed this bug with you. On further investigation it appears that this issue is due to there being a command line switch AND a subroutine called profile. In a nutshell, the subroutine “align” calls “_setparams” which in turn runs through all items in @MUSCLE_SWITCHES, which includes the switch “profile”. In this loop the line "$value = $self->$attr()” sets the internal parameters for the object. The issue is that there is also a subroutine called “profile” which is called when a profile-profile alignment is requested by the user. This subroutine is erroneously called at this point and throws the error below as a result. I fixed this by changing the name of the subroutine and any reference to it, to “runprofile”. Kind regards, Richard Show quoted text
> On 7 Aug 2017, at 9:07 am, Bugs in bioperl-run via RT <bug-bioperl-run@rt.cpan.org> wrote: > > > Greetings, > > This message has been automatically generated in response to the > creation of a trouble ticket regarding: > "Bio::Tools::Run::Alignment::Muscle profile line 320", > a summary of which appears below. > > There is no need to reply to this message right now. Your ticket has been > assigned an ID of [rt.cpan.org #122733]. Your ticket is accessible > on the web at: > > https://rt.cpan.org/Ticket/Display.html?id=122733 > > Please include the string: > > [rt.cpan.org #122733] > > in the subject line of all future correspondence about this issue. To do so, > you may reply to this message. > > Thank you, > bug-bioperl-run@rt.cpan.org > > ------------------------------------------------------------------------- > Dear all, > > On line 320 in Bio::Tools::Run::Alignment::Muscle is a throw() that prevents versions of muscle other than v3.52 from being run with this module. > The error "profile does not work for this version of muscle” is returned. > > I looks like this was added to avoid segfaults in profile-profile alignments in early v3.6 releases of Muscle. The software is at v3.8.31 at the moment. > I am not doing profile-profile alignments in my work and so cannot check to see if this aspect of muscle is stable but if the developers of muscle have resolved these issues then it would be great if this throw() could be removed to allow newer versions of muscle to be used with this module. > > Kind regards, > Richard
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This is now fix on github master (commit c71bab3). Thanks for pointing this out! On Mon Aug 07 03:11:42 2017, Richard.Francis@telethonkids.org.au wrote: Show quoted text
> Dear all, > > I just filed this bug with you. > On further investigation it appears that this issue is due to there > being a command line switch AND a subroutine called profile. > > In a nutshell, the subroutine “align” calls “_setparams” which in turn > runs through all items in @MUSCLE_SWITCHES, which includes the switch > “profile”. > In this loop the line "$value = $self->$attr()” sets the internal > parameters for the object. The issue is that there is also a > subroutine called “profile” which is called when a profile-profile > alignment is requested by the user. This subroutine is erroneously > called at this point and throws the error below as a result. > > I fixed this by changing the name of the subroutine and any reference > to it, to “runprofile”. > > Kind regards, > Richard > >
> > On 7 Aug 2017, at 9:07 am, Bugs in bioperl-run via RT <bug-bioperl- > > run@rt.cpan.org> wrote: > > > > > > Greetings, > > > > This message has been automatically generated in response to the > > creation of a trouble ticket regarding: > > "Bio::Tools::Run::Alignment::Muscle profile line 320", > > a summary of which appears below. > > > > There is no need to reply to this message right now. Your ticket has > > been > > assigned an ID of [rt.cpan.org #122733]. Your ticket is accessible > > on the web at: > > > > https://rt.cpan.org/Ticket/Display.html?id=122733 > > > > Please include the string: > > > > [rt.cpan.org #122733] > > > > in the subject line of all future correspondence about this issue. To > > do so, > > you may reply to this message. > > > > Thank you, > > bug-bioperl-run@rt.cpan.org > > > > ------------------------------------------------------------------------- > > Dear all, > > > > On line 320 in Bio::Tools::Run::Alignment::Muscle is a throw() that > > prevents versions of muscle other than v3.52 from being run with this > > module. > > The error "profile does not work for this version of muscle” is > > returned. > > > > I looks like this was added to avoid segfaults in profile-profile > > alignments in early v3.6 releases of Muscle. The software is at > > v3.8.31 at the moment. > > I am not doing profile-profile alignments in my work and so cannot > > check to see if this aspect of muscle is stable but if the developers > > of muscle have resolved these issues then it would be great if this > > throw() could be removed to allow newer versions of muscle to be used > > with this module. > > > > Kind regards, > > Richard
>


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