[BioRuby] Blast Format8 hsps' patch
Toshiaki Katayama
ktym at hgc.jp
Mon Sep 3 14:11:40 UTC 2007
Hi Raoul,
Thank you for pointing this bug out.
I think I fixed this problem but for double check,
could you personally send me your patch as a separate mail?
This list doesn't allow attachments.
Regards,
Toshiaki
On 2007/08/29, at 18:21, Raoul Jean Pierre Bonnal wrote:
> Hi Guys,
> I found a bug in the parser. Take this example:
>
>
> contig00002 gi|15902044|ref|NC_003098.1| 99.71 1399 4
> 0 5 1403 414678 416076 0.0 2742
> contig00002 gi|118090026|ref|NC_003028.2| 98.25 858 5
> 1 556 1403 448891 449748 0.0 1592
> contig00003 gi|116515308|ref|NC_008533.1| 99.67 2997 7
> 2 1 2994 423818 426814 0.0 5848
> contig00003 gi|15902044|ref|NC_003098.1| 99.67 2997 7
> 2 1 2994 416288 419284 0.0 5848
> contig00003 gi|118090026|ref|NC_003028.2| 99.60 2997 9
> 2 1 2994 449959 452955 0.0 5832
> contig00004 gi|118090026|ref|NC_003028.2| 98.08 2238 40
> 3 5 2242 453000 455234 0.0 4072
> contig00004 gi|116515308|ref|NC_008533.1| 97.94 2238 43
> 3 5 2242 426859 429093 0.0 4048
> contig00004 gi|15902044|ref|NC_003098.1| 97.94 2238 43
> 3 5 2242 419329 421563 0.0 4048
>
>
> about last contig00003 the parser create an hit with 2 hsps, putting
> togheter results from last contig00003 and first contig00004, this is
> wrong. The code check only if the target is different from the prev one,
> in this case the target is the same but the query is different.
>
> In attach the patch to solve the problem, I put a chk on the query too.
>
> Actually I don't know if the problem is present with other parsers.
>
> Best regards.
>
> --
> Ra
>
>
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