[BioRuby] Blast Format8 hsps' patch
Raoul Jean Pierre Bonnal
raoul.bonnal at itb.cnr.it
Wed Aug 29 09:21:09 UTC 2007
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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