[Bioperl-l] problems with parsing hmmpfam

[Jason Stajich]

bioperl 1.2.2 and bioperl-live in CVS will parse these reports fine as far
as I can tell so I would suggest upgrading to bioperl 1.2.2

-jason

On Fri, 1 Aug 2003, Sofia wrote:

> I am trying to parse a hmmpfam report.  I am mostly sucessful until I have the following error:
>
>
> Use of uninitialized value in array element at /usr/lib/perl5/site_perl/5.8.0/Bio/SearchIO/hmmer.pm line 488, <GEN1> line 56473.
>
> ------------- EXCEPTION  -------------
> MSG: Somehow the Model table order does not match the order in the domains (got [no, expected AFP)
> STACK Bio::SearchIO::hmmer::next_result /usr/lib/perl5/site_perl/5.8.0/Bio/SearchIO/hmmer.pm:489
> STACK toplevel ./parseHMM.pl:8
>
> --------------------------------------
> It seems to only occur when my scores for sequence family classification is "no hits above threshold" and my parsed for domains has a hit (though usually very poor score).
>
> How can I filter out these records with SearchIO?
>
> Thanks,
> Sofia
>
>
> Output which causes me to have this error
> -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> Query sequence: 26SrRNA
> Accession:      [none]
> Description:    [none]
>
> Scores for sequence family classification (score includes all domains):
> Model    Description                                    Score    E-value  N
> -------- -----------                                    -----    ------- ---
>         [no hits above thresholds]
>
> Parsed for domains:
> Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
> -------- ------- ----- -----    ----- -----      -----  -------
> AFP        1/1     268   279 ..     1    12 []     0.3       89
>
> Alignments of top-scoring domains:
> AFP: domain 1 of 1, from 268 to 279: score 0.3, E = 89
>                    *->tCTgStnCteAt<-*
>                       tCT +t Ct+A
>      26SrRNA   268    TCTCGTACTGAG    279
>
> //
>
> Query sequence: 40Sribosomal.protS11
> Accession:      [none]
> Description:    [none]
>
> Scores for sequence family classification (score includes all domains):
> Model    Description                                    Score    E-value  N
> -------- -----------                                    -----    ------- ---
>         [no hits above thresholds]
>
> Parsed for domains:
> Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
> -------- ------- ----- -----    ----- -----      -----  -------
> AFP        1/1     127   138 ..     1    12 []     1.7       53
>
> Alignments of top-scoring domains:
> AFP: domain 1 of 1, from 127 to 138: score 1.7, E = 53
>                    *->tCTgStnCteAt<-*
>                       + Tg+tnC +
>   40Sribosom   127    AATGGTNCATTA    138
>
> //
> -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu