[Bioperl-l] Fwd: edit to PAML.pm

[Dave Messina]

Hi Volker,

Your revert does work for yn00 output, but unfortunately breaks the code
for another type of output (see Bug 3332,
https://redmine.open-bio.org/issues/3332), one of many horrendous format
issues PAML brings.

I've committed a fix (12ddb53) that does special case parsing for yn00. I
haven't tested it extensively, so please don't hesitate to try it out and
submit an improved version via pull request at github if need be.


Best,
Dave



On Thu, Mar 27, 2014 at 6:01 PM, Jason Stajich <jason at bioperl.org> wrote:

> Hi - great to hear that it is still useful - I have long stopped having
> time to try and track the versions of PAML and the output changes so that
> our parser will work better.
>
>  I am CC-ing Dave Messina who was the last person to touch this module I
> believe as he may be able to take a look at it and contribute - this looks
> extra simple so it may be easy enough for Dave or someone else to do this
> fix.
>
>  I would encourage you to contribute fixes directly in the future if you
> can at the github repository -- esp if you are using the module and are
> undoubtable hitting some issues with the format.
>
> Thanks,
> Jason
>
> Jason Stajich
> jason at bioperl.org
> http://bioperl.org/wiki/User:Jason
> http://twitter.com/hyphaltip
>
>
> On Mon, Mar 24, 2014 at 5:31 PM, Volker Brendel <vbrendel at iastate.edu>wrote:
>
>> Hi Jason,
>>
>> I am still using your BioPerl code that runs PAML and parses the program
>> output.  One of my workflows failed on a new installation, but ran ok on an
>> older installation, and after a bit of searching I traced the error to the
>> following lines in PAML.pm.  These lines parse a table in the PAM output.
>>  The older version of PAML.pm parsed the first line correctly, while the
>> new version fails (it assumes that there is more than the species label on
>> each line, including the first).  I reverted to the old parsing, and all is
>> well (presumably, as I don't know whether something else required the
>> change for other reasons).  Thus, I propose to revert to the old code, as I
>> did in the record below (PAML.pm is what I think it should be, PAML.pmORIG
>> what is in BioPerl right now).
>>
>> Hope this makes sense.
>> Best, Volker
>>
>> /usr/local/share/perl5/Bio/Tools/Phylo
>>
>> Gerp.pm  Gumby.pm  Molphy  Molphy.pm  PAML  PAML.pm  PAML.pmORIG Phylip
>>
>> Fri Mar 21 21:28:05 EDT 2014
>>
>> []#diff PAML.pm*
>> 907c907,909
>> <         my ( $seq, $rest ) = split( /\s+/, $_, 2 );
>> ---
>> >         $_ =~ m/(.+?)\s*(-*\d+?\.\d+?.*)/;
>> >          my $seq = $1;
>> >          my $rest = $2;
>> []#
>>
>> will correctly parse a table like the following (produced by yn00):
>>
>> Nei & Gojobori 1986. dN/dS (dN, dS)
>> Am
>> Bt               0.076(0.0603 0.7926)
>>
>>
>> --
>> Volker Brendel
>> Professor of Biology and Computer Science
>> Indiana University
>> Department of Biology & School of Informatics and Computing
>> 212 South Hawthorne Drive
>> Simon Hall 205C
>> Bloomington, IN 47405
>>
>> Tel.: (812) 855-7074
>> http://brendelgroup.org/
>>
>>
>