[Bioperl-l] Bio::Search results

Sean O'Keeffe limericksean at gmail.com
Tue Aug 30 11:28:11 EDT 2005


Hi Barry, thanks for the reply. Below is a snippet of the file (I
generated it with hmmpfam using the alignment flag set to -A 0, to
remove alignments - this shouldn't affect the parsing of the file) :

hmmpfam - search one or more sequences against HMM database
HMMER 2.3.2 (Oct 2003)
Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
Freely distributed under the GNU General Public License (GPL)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file:                 /usr/local/lib/pfam-tm
Sequence file:            Mus_musculus.NCBIM34.jul.pep.fa-short
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query sequence: ENSMUSP00000089702
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
-------- ------- ----- -----    ----- -----      -----  -------
	[no hits above thresholds]
//

Query sequence: ENSMUSP00000089701
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
-------- ------- ----- -----    ----- -----      -----  -------
	[no hits above thresholds]
//

Query sequence: ENSMUSP00000020094
Accession:      [none]
Description:    [none]

Scores for sequence family classification (score includes all domains):
Model    Description                                    Score    E-value  N 
-------- -----------                                    -----    ------- ---
LRR_1    Leucine Rich Repeat                             55.0    3.7e-15   6
LRRNT    Leucine rich repeat N-terminal domain           30.1    1.1e-07   1

Parsed for domains:
Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
-------- ------- ----- -----    ----- -----      -----  -------
LRRNT      1/1     117   142 ..     1    34 []    30.1  1.1e-07
LRR_1      1/6     168   191 ..     1    25 []    14.7   0.0049
LRR_1      2/6     192   210 ..     1    25 []     9.1      0.2
LRR_1      3/6     212   237 ..     1    25 []     8.4     0.26
LRR_1      4/6     238   257 ..     1    25 []    10.3      0.1
LRR_1      5/6     259   282 ..     1    25 []    10.1     0.12
LRR_1      6/6     290   314 ..     1    25 []     2.4        2
//

Query sequence: ENSMUSP00000074175
Accession:      [none]
Description:    [none]

Scores for sequence family classification (score includes all domains):
Model    Description                                    Score    E-value  N 
-------- -----------                                    -----    ------- ---
CUB      CUB domain                                     232.5    1.3e-68   2
Trypsin  Trypsin                                        206.0    1.2e-60   1
Sushi    Sushi domain (SCR repeat)                       88.7    2.6e-25   2
EGF_CA   Calcium binding EGF domain                      29.4    1.8e-07   1

Parsed for domains:
Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
-------- ------- ----- -----    ----- -----      -----  -------
CUB        1/2      16   137 ..     1   116 []    70.0  1.1e-19
EGF_CA     1/1     141   188 ..     1    55 []    29.4  1.8e-07
CUB        2/2     192   301 ..     1   116 []   162.5  1.5e-47
Sushi      1/2     308   370 ..     1    62 []    47.5  6.5e-13
Sushi      2/2     375   446 ..     1    62 []    41.2  5.1e-11
Trypsin    1/1     463   698 ..     1   259 []   206.0  1.2e-60
//


Cheers,
Sean.



On 8/30/05, Barry Moore <bmoore at genetics.utah.edu> wrote:
> Sean,
> 
> Don't see anything obviously wrong.  If you want to send your input
> file, I'll try to recreate the problem.
> 
> Barry
> 
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Sean
> O'Keeffe
> Sent: Tuesday, August 30, 2005 2:55 AM
> To: bioperl-l at portal.open-bio.org
> Subject: [Bioperl-l] Bio::Search results
> 
> Hi,
> The following code snippet is something I use to extract information
> from hmmer result files:
> 
> use Bio::SearchIO;
> 
> my $in =3D new Bio::SearchIO( -format =3D> 'hmmer',  -file =3D> $ARGV[0]
> );
> while(my $result =3D $in->next_result) {
>   print $result->query_name(), "\n",$result->query_description(),"\n";
>   while (my $hit =3D $result->next_hit) {
>     while(my $hsp =3D $hit->next_domain) {
>       next unless ($hsp->name =3D~ /^ig|^lrr|^fn3|^egf|^tsp|^psi/i);
>       print $hsp->start(),"\t",$hsp->end(),"\t",$hsp->evalue(),"\n";
>     }
>   }
> }
> 
> The input file is generated by hmmpfam and is given at the command
> line. I use it to scan for specific domain names e.g ig, fn3 lrr etc.
> This code works for the first loop and then ends so I get the name and
> description (no hsp values as their are none for this result):
> 
> ENSMUSP00000065602=20
> pep:novel supercontig::NT_085813:405:1510:-1 gene:ENSMUSG00000054059
> transcript:ENSMUST00000066517
> 
> My question is why does the loop end after one instance. Incidentally
> the outputted  name and description above are the last ones in the
> hmmer file (maybe the file is read from the back??? - don't know if this
> means anything).
> Any thoughts would be appreciated. Thanks,
> Sean.
> 
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