From: Arnaud K. <ax...@sa...> - 2004-08-09 14:18:05
|
Hi I've got a script from Pablo Mendes called parseBlastFilesForSimilarity.pl that uses CBIL::Bio::Blast::BlastAnal module part of the CBIL distribution. To make the blast parsing work for me (to parse the score), I had to do a minor modification, line 131: if (/... \s(\d+) .../) { by if (/... \s+(\d+) .../) { ie match at least one space before parsing the score value, instead of matching one and only one space. Also, in the BLAST output, the query and subject ids are meant to be GUS Primary keys, I have instead the real subject and query identifiers. In LoadBlastSimFast.pm, could we make the parsing more generic so it can accept both ? I have made the changes locally, I can commit an update if nobody minds. Shall I make sourceforge entries to log them ? cheers Arnaud |
From: Steve F. <sfi...@pc...> - 2004-08-09 15:40:28
|
arnaud- i will make the change to BlastAnal and release a new .tar for the CBIL code. go ahead and commit your fix to LoadBlastSimFast.pm steve Arnaud Kerhornou wrote: > Hi > > I've got a script from Pablo Mendes called > parseBlastFilesForSimilarity.pl that uses CBIL::Bio::Blast::BlastAnal > module part of the CBIL distribution. To make the blast parsing work > for me (to parse the score), I had to do a minor modification, line 131: > if (/... \s(\d+) .../) { > by > if (/... \s+(\d+) .../) { > > ie match at least one space before parsing the score value, instead of > matching one and only one space. > > Also, in the BLAST output, the query and subject ids are meant to be > GUS Primary keys, I have instead the real subject and query identifiers. > In LoadBlastSimFast.pm, could we make the parsing more generic so it > can accept both ? I have made the changes locally, I can commit an > update if nobody minds. > > Shall I make sourceforge entries to log them ? > > cheers > Arnaud > > > ------------------------------------------------------- > This SF.Net email is sponsored by OSTG. Have you noticed the changes on > Linux.com, ITManagersJournal and NewsForge in the past few weeks? Now, > one more big change to announce. We are now OSTG- Open Source Technology > Group. Come see the changes on the new OSTG site. www.ostg.com > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
From: Arnaud K. <ax...@sa...> - 2004-08-11 13:30:28
|
Hi Steve Fischer wrote: > arnaud- > > i will make the change to BlastAnal and release a new .tar for the > CBIL code. > > go ahead and commit your fix to LoadBlastSimFast.pm > I have commited an updated version of LoadBlastSimFast plugin. It can also parse the real subject and query identifiers and get the primary keys associated with them. It shouldn't affect the parsing if the primary keys are already in the BLAST formated output. If not let me know. cheers Arnaud > steve > > Arnaud Kerhornou wrote: > >> Hi >> >> I've got a script from Pablo Mendes called >> parseBlastFilesForSimilarity.pl that uses CBIL::Bio::Blast::BlastAnal >> module part of the CBIL distribution. To make the blast parsing work >> for me (to parse the score), I had to do a minor modification, line 131: >> if (/... \s(\d+) .../) { >> by >> if (/... \s+(\d+) .../) { >> >> ie match at least one space before parsing the score value, instead >> of matching one and only one space. >> >> Also, in the BLAST output, the query and subject ids are meant to be >> GUS Primary keys, I have instead the real subject and query identifiers. >> In LoadBlastSimFast.pm, could we make the parsing more generic so it >> can accept both ? I have made the changes locally, I can commit an >> update if nobody minds. >> >> Shall I make sourceforge entries to log them ? >> >> cheers >> Arnaud >> |
From: Steve F. <sfi...@pc...> - 2004-08-09 16:06:59
|
i have updated the cbil .tar with the change below. it is in v1-6-0. steve Arnaud Kerhornou wrote: > Hi > > I've got a script from Pablo Mendes called > parseBlastFilesForSimilarity.pl that uses CBIL::Bio::Blast::BlastAnal > module part of the CBIL distribution. To make the blast parsing work > for me (to parse the score), I had to do a minor modification, line 131: > if (/... \s(\d+) .../) { > by > if (/... \s+(\d+) .../) { > > ie match at least one space before parsing the score value, instead of > matching one and only one space. > > Also, in the BLAST output, the query and subject ids are meant to be > GUS Primary keys, I have instead the real subject and query identifiers. > In LoadBlastSimFast.pm, could we make the parsing more generic so it > can accept both ? I have made the changes locally, I can commit an > update if nobody minds. > > Shall I make sourceforge entries to log them ? > > cheers > Arnaud > > > ------------------------------------------------------- > This SF.Net email is sponsored by OSTG. Have you noticed the changes on > Linux.com, ITManagersJournal and NewsForge in the past few weeks? Now, > one more big change to announce. We are now OSTG- Open Source Technology > Group. Come see the changes on the new OSTG site. www.ostg.com > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
From: Arnaud K. <ax...@sa...> - 2004-08-09 16:08:49
|
Hi Steve Steve Fischer wrote: > i have updated the cbil .tar with the change below. it is in v1-6-0. > thanks > steve > > Arnaud Kerhornou wrote: > >> Hi >> >> I've got a script from Pablo Mendes called >> parseBlastFilesForSimilarity.pl that uses CBIL::Bio::Blast::BlastAnal >> module part of the CBIL distribution. To make the blast parsing work >> for me (to parse the score), I had to do a minor modification, line 131: >> if (/... \s(\d+) .../) { >> by >> if (/... \s+(\d+) .../) { >> >> ie match at least one space before parsing the score value, instead >> of matching one and only one space. >> >> Also, in the BLAST output, the query and subject ids are meant to be >> GUS Primary keys, I have instead the real subject and query identifiers. >> In LoadBlastSimFast.pm, could we make the parsing more generic so it >> can accept both ? I have made the changes locally, I can commit an >> update if nobody minds. >> will commit my update >> Shall I make sourceforge entries to log them ? >> >> cheers >> Arnaud >> cheers Arnaud |