[Bioperl-l] problems with parsing hmmpfam

[Sofia]

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  

//
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