[Bioperl-l] RE:Segmentation fault

[Jason Stajich]

So... if you run my example code against your file you get a segfault?

If this is the case you need to attach the exact file (perhaps compressed
as well) to a new bugreport at http://bugzilla.open-bio.org/. Don't copy
and paste the report into the bug, but attach it to the bug report.
Preferably the smallest report which still causes the segfault.

Need to know which version of bioperl you are running too...

-jason

On Mon, 12 Apr 2004, stephan rosecker wrote:

>  > I really have no idea what you are doing....
>
> :-)
> I got an protein-profile-file build with hmmer. (nst.hmms).
> So i use hmmpfam with a flatfile database "uniprot_sprot.dat" to find
> proteins compatible with my profile.
> (hmmpfam -A0 -E1e-30 nst.hmms uniprot_sprot.dat > hmmerresultfile.out)
> So each result contains a hit or more is what i need.
>
>
>
> This for example is good: (hmmerresultfile.out)
>
> //
>
> Query sequence: 128U_DROME
> Accession:      P32234
> Description:    GTP-binding protein 128UP.
>
> Scores for sequence family classification (score includes all domains):
> Model    Description                                    Score    E-value  N
> -------- -----------                                    -----    ------- ---
> Drg                                                     639.4   1.6e-191   1
>
> Parsed for domains:
> Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
> -------- ------- ----- -----    ----- -----      -----  -------
> Drg        1/1       4   367 ..     1   375 []   639.4 1.6e-191
>
> Alignments of top-scoring domains:
> Drg: domain 1 of 1, from 4 to 367: score 639.4, E = 1.6e-191
>                     *->GIeEkIkaIEeEiarTqKNKATEyHLGlLKaKLAkLReQLlEpskgg
>                         I+EkI aIE E+arTqKNKAT  HLGlLKa  AkLR +L   s +g
>    128U_DROME     4    -ILEKISAIESEMARTQKNKATSAHLGLLKANVAKLRRELI--SPKG 47
>
>                     gGGG...kGFeVeKSGdarvaLIGfPSVGKStLLakLTntkSEvAdYaFT
>                     gGGG+++ GFeV+K Gdarv ++GfPSVGKStLL+ L +  SEvA+Y+FT
>    128U_DROME    48 GGGGtgeAGFEVAKTGDARVGFVGFPSVGKSTLLSNLAGVYSEVAAYEFT 97
>
>                     TLTcvPGvLeYqgakIQllDlPGIIeGAssGKGRGrqVlAvarsADLvLm
>                     TLT vPG ++Y+gakIQllDlPGIIeGA  GKGRGrqV+Avar+  L+ m
>    128U_DROME    98 TLTTVPGCIKYKGAKIQLLDLPGIIEGAKDGKGRGRQVIAVARTCNLIFM 147
>
>                     vLDatkleehrdvLekELEnVGIRLnkrkGPniyfKkKetGGvsvngTgp
>                     vLD  k+ +h  +Le ELE  GIRLnk++ Pniy+K K  GG++ n+ +p
>    128U_DROME   148 VLDCLKPLGHKKLLEHELEGFGIRLNKKP-PNIYYKRKDKGGINLNSMVP 196
>
>                     PLThidEdtvrrILheYRIhNAeVliReDqvTlDdFIDVVnegNRvYipc
>                        ++d d+v++IL+eY+IhNA++  R D +T Dd IDV+ egNR Yipc
>    128U_DROME   197 -QSELDTDLVKTILSEYKIHNADITLRYD-ATSDDLIDVI-EGNRIYIPC 243
>
>                     LyVyNKIDlvgieevdrlarkrlEiGpntIVvScnmglnLdelaerlwek
>                     +y +NKID+++iee+d + +      p  + +S+    n d+l+e +we
>    128U_DROME   244 IYLLNKIDQISIEELDVIYKI-----PHCVPISAHHHWNFDDLLELMWEY 288
>
>                     LglvRVYtKkqGkePDFDPLvepLilRrGsT.VeDvChhiHrDLvrrFKY
>                     L l R+YtK++G+ PD+     p +l +  T++eD+C+++Hr  +++FKY
>    128U_DROME   289 LRLQRIYTKPKGQLPDYN---SPVVLHNERTsIEDFCNKLHRSIAKEFKY 335
>
>                     AlVWGkSaKhppQrVGleHvleDeDvvqivvK<-*
>                     AlVWG+S+Kh pQ+VG+eHvl DeDvvqiv+K
>    128U_DROME   336 ALVWGSSVKHQPQKVGIEHVLNDEDVVQIVKK    367
>
> //
>
>
> This for example is useless: (hmmerresultfile.out)
>
> //
> Query sequence: 10KD_VIGUN
> Accession:      P18646
> Description:    10 kDa protein precursor (Clone PSAS10).
>
> 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
> -------- ------- ----- -----    ----- -----      -----  -------
>          [no hits above thresholds]
>
> Alignments of top-scoring domains:
>          [no hits above thresholds]
> //
>
>
>
>
>
> best regards,
> stephan
>
>
>
>
>
>
>
>  >
>  >
>  > If you want to initialize a SearchIO parser to read in HMMER output
>  > results you do
>  >
>  > my $in = Bio::SearchIO(-file => 'hmmerresultfile.out',
>  >                        -format => 'hmmer');
>  >
>  > # an loop through each result (a single result per query sequence)
>  > while( my $result = $in->next_result ) {
>  >   # print the query name
>  >   # for hmmpfam this will be each sequence in the input set
>  >   # for hmmsearch this will be the name of the HMM file you
>  >   # used to search
>  >   print $result->query_name, "\n";
>  >
>  >   # now print all the hits (for HMMPFAM this will be the Pfam domains
>  >   # for hmmsearch this will be the sequences in the db that had good
>  >   # alignments
>  >   while ( my $hit = $result->next_hit ) {
>  >     # print the name, indented with a tab
>  >     print "\t", $hit->name, "\n";
>  >   }
>  > }
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

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