[Bioperl-l] BUG

[Fields, Christopher J]

fangl,

It would help if you can post a bug report on this, just to make sure we can reproduce it.  Attach an example data set and code.

https://redmine.open-bio.org/

chris

On Apr 15, 2013, at 3:13 AM, fangl <fangl at big.ac.cn>
 wrote:

> Hi,
> I find a bug when I use Bio::SearchIO to parse Hmmscan.
> The result of my Hmmscan has 2 hits against 1 query ,but the module of Bio::SearchIO can only parse 1 hit in the output file.
> eg:
> hmmscan result:
> # hmmscan :: search sequence(s) against a profile database
> # HMMER 3.0 (March 2010); http://hmmer.org/
> # Copyright (C) 2010 Howard Hughes Medical Institute.
> # Freely distributed under the GNU General Public License (GPLv3).
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # query sequence file:             pro_2.fa
> # target HMM database:             /leofs/biodenovo/fangl/data/Pfam/Pfam-A.hmm
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> 
> Query:       PEG03688  [L=200]
> Scores for complete sequence (score includes all domains):
>   --- full sequence ---   --- best 1 domain ---    -#dom-
>    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
>    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
>    0.00038   20.7   0.1    0.00054   20.2   0.1    1.3  1  SnoaL_2       SnoaL-like domain
>  ------ inclusion threshold ------
>      0.068   12.9   0.0       0.43   10.3   0.0    2.0  1  FAD_binding_8 FAD-binding domain
> 
> 
> Domain annotation for each model (and alignments):
>>> SnoaL_2  SnoaL-like domain
>   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
> ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
>   1 !   20.2   0.1   7.9e-08   0.00054      11      86 ..      59     157 ..      46     172 .. 0.72
> 
>  Alignments for each domain:
>  == domain 1    score: 20.2 bits;  conditional E-value: 7.9e-08
>               T-HHHHHHTEEEEEEEE............CT.S--..E---HHHHHHHTTHHHCEECEEEEEEEEESSTTEEEEEEEEE-E........ESBS--EEEE CS
>   SnoaL_2  11 gdldalaallapdvvwe............dp.fge..lrGrealraffrallaafpdlrfevedviadgdrvvvrwtvtgt........ipptgrgvtv 86 
>                d   l +l++ d+++             +p +g+  + G++a+ + f ++   +    f+++++++d+  v++++ +t+t        i p  ++ +v
>  PEG03688  59 PDYNLLKELVTYDCTYIsltfdnptlhgiMPwAGThtHVGPQAFIDIFTRVGLYWDRGPFSIDHIFGDDGNVTAWGSFTATsrtlgktvISPWAARARV 157
>               3666888999999999877777555545545544488******************************************98555555554444444444 PP
> 
>>> FAD_binding_8  FAD-binding domain
>   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
> ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
>   1 ?   10.3   0.0   6.3e-05      0.43      19      63 ..      77     128 ..      63     197 .. 0.69
> 
>  Alignments for each domain:
>  == domain 1    score: 10.3 bits;  conditional E-value: 6.3e-05
>  FAD_binding_8  19 lklkkpkks.......lkykpGqyvfini.pslsklflqsHPFtiasapeddk 63 
>                    l++  p+         ++ + G  +fi i  ++  l+++  PF+i     dd 
>       PEG03688  77 LTFDNPTLHgimpwagTHTHVGPQAFIDIfTRVG-LYWDRGPFSIDHIFGDDG 128
>                    555555444444444468899999*****66666.99********88777664 PP
> 
> 
> 
> Internal pipeline statistics summary:
> -------------------------------------
> Query sequence(s):                         1  (200 residues)
> Target model(s):                       13672  (2396357 nodes)
> Passed MSV filter:                       244  (0.0178467); expected 273.4 (0.02)
> Passed bias filter:                      219  (0.0160181); expected 273.4 (0.02)
> Passed Vit filter:                        14  (0.00102399); expected 13.7 (0.001)
> Passed Fwd filter:                         2  (0.000146284); expected 0.1 (1e-05)
> Initial search space (Z):              13672  [actual number of targets]
> Domain search space  (domZ):               2  [number of targets reported over threshold]
> # CPU time: 0.15u 0.13s 00:00:00.28 Elapsed: 00:00:06.72
> # Mc/sec: 71.32
> //
> 
> my parse result:
> query len hit len query_start query_end query_match_len hit_start hit_end hit_match_len evalue cov
> PEG03688 200 SnoaL_2 0 59 157 99 11 86 76 7.9e-08 0.49
> 
> 
> pleast to solve this problem!
> Thanks!
> 
> Best wishes!
> 
> 
> 
> fangl
> 
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