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A question about iBio::Index: and its correct use
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A question about iBio::Index: and its correct use
by jluis.lavin
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Hello to all, I´m trying to write a script to retrieve a list of sequences from a local FASTA file (for example a fasta archive where all the protein models of an organism are stored). This file would be used by me as some kind "local database" (sorry if I mistake a few concepts...) I´ve been reading the BioPerl HOWTOs and I came across the Bio::Index::Fasta tool. If I didn´t misunderstood what I read (which can be easy because my low level on programming) this Indexing tool should do the job. I wrote a couple of scripts based on the documentation i read about this tool, but I don´t seem to be able to create the index file to be used later (to retrieve the sequences from). -First of all, I want to ask the people in this forum if the Bio::Index::Fasta is the right one to chose for this tasks. -Then I´ll beg you to take a look at my scripts, because I don´t seem to catch the bug... Best wishes to you all and thanks in advance ;) -- José Luis Lavín Trueba, PhD Dpto. de Producción Agraria Grupo de Genética y Microbiología Universidad Pública de Navarra 31006 Pamplona Navarra SPAIN _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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Re: A question about iBio::Index: and its correct use
by Mark A. Jensen
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José -- It looks like this is a good solution to your problem. Please send you
script so we can look at it- cheers Mark ----- Original Message ----- From: <jluis.lavin@...> To: <bioperl-l@...> Sent: Thursday, November 05, 2009 10:28 AM Subject: [Bioperl-l] A question about iBio::Index: and its correct use Hello to all, I´m trying to write a script to retrieve a list of sequences from a local FASTA file (for example a fasta archive where all the protein models of an organism are stored). This file would be used by me as some kind "local database" (sorry if I mistake a few concepts...) I´ve been reading the BioPerl HOWTOs and I came across the Bio::Index::Fasta tool. If I didn´t misunderstood what I read (which can be easy because my low level on programming) this Indexing tool should do the job. I wrote a couple of scripts based on the documentation i read about this tool, but I don´t seem to be able to create the index file to be used later (to retrieve the sequences from). -First of all, I want to ask the people in this forum if the Bio::Index::Fasta is the right one to chose for this tasks. -Then I´ll beg you to take a look at my scripts, because I don´t seem to catch the bug... Best wishes to you all and thanks in advance ;) -- José Luis Lavín Trueba, PhD Dpto. de Producción Agraria Grupo de Genética y Microbiología Universidad Pública de Navarra 31006 Pamplona Navarra SPAIN _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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Re: A question about iBio::Index: and its correct use
by Hotz, Hans-Rudolf-2
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Jluis > -Then I´ll beg you to take a look at my scripts, because I don´t seem to > catch the bug... you haven't attached/included any scripts, have you? Anyway, have you considered using BLAST indices (created with the additional flag "-o") together with the tool 'fastacmd' (which also included in the NCBI blast binaries) as a simple (and very fast) alternative for fetching sequences. Regards, Hans _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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Re: A question about iBio::Index: and its correct use
by jluis.lavin
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Thanks a lot for your help Hans,
It's a little bit to hard to understand and turn into script this awesome information you've just given me...I hope I can use it in a near future anyway ;) The issue here is that the sequences I,m indexing are not generated by the NCBI nor stored there...although I belive you´re just refering to the tool itself and not to a retrieval from the NCBI. Thanks again you´re all great giving advice to newbies like me ;) Best wishes to you all El Jue, 5 de Noviembre de 2009, 17:02, Hotz, Hans-Rudolf escribió: > > > > Jluis > >> -Then I´ll beg you to take a look at my scripts, because I don´t seem to >> catch the bug... > > you haven't attached/included any scripts, have you? > > > Anyway, have you considered using BLAST indices (created with the > additional > flag "-o") together with the tool 'fastacmd' (which also included in the > NCBI blast binaries) as a simple (and very fast) alternative for fetching > sequences. > > > Regards, Hans > > > -- Dr. José Luis Lavín Trueba Dpto. de Producción Agraria Grupo de Genética y Microbiología Universidad Pública de Navarra 31006 Pamplona Navarra SPAIN _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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Re: A question about iBio::Index: and its correct use
by Florent Angly
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Hans-Rudolf was talking about a way to retrieve sequences from a BLAST
database. If you use BLAST locally, then your database is local too. More info here: http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/formatdb_fastacmd.html Florent jluis.lavin@... wrote: > Thanks a lot for your help Hans, > It's a little bit to hard to understand and turn into script this awesome > information you've just given me...I hope I can use it in a near future > anyway ;) > The issue here is that the sequences I,m indexing are not generated by the > NCBI nor stored there...although I belive you´re just refering to the tool > itself and not to a retrieval from the NCBI. > > Thanks again you´re all great giving advice to newbies like me ;) > > Best wishes to you all > > > El Jue, 5 de Noviembre de 2009, 17:02, Hotz, Hans-Rudolf escribió: > >> >> Jluis >> >> >>> -Then I´ll beg you to take a look at my scripts, because I don´t seem to >>> catch the bug... >>> >> you haven't attached/included any scripts, have you? >> >> >> Anyway, have you considered using BLAST indices (created with the >> additional >> flag "-o") together with the tool 'fastacmd' (which also included in the >> NCBI blast binaries) as a simple (and very fast) alternative for fetching >> sequences. >> >> >> Regards, Hans >> >> >> >> > > > _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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Re: A question about iBio::Index: and its correct use
by jluis.lavin
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Thank you for the info Florent!
I´ll try to read al the information on the link you provided and try to figure out how to make it work and if it is worthy for me, I mean, I work with several sequence files that come from multiple databases (JGI, BROAD, Genolevures or NCBI). Protein IDs from each of those databases is different from NCBI. Maybe it could be easier to write a script that allows me to enter a fasta file with all the protein models of a single organism, parse it and then extract the sequences of a given list (using the "ID style" of the particular database) than creating a BLAST index for each organism I need to work with...Did I explain the issue correctly? Anyway, since I don´t know anything about this tool Hans and you provided me, I can easily be wrong... Thank you for showing me the local BLAST Index tool, I´ll read the documentation carefully and study all its possibilities. Best wishes JL El Jue, 5 de Noviembre de 2009, 19:00, Florent Angly escribió: > Hans-Rudolf was talking about a way to retrieve sequences from a BLAST > database. If you use BLAST locally, then your database is local too. > More info here: > http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/formatdb_fastacmd.html > Florent > > > jluis.lavin@... wrote: >> Thanks a lot for your help Hans, >> It's a little bit to hard to understand and turn into script this >> awesome >> information you've just given me...I hope I can use it in a near future >> anyway ;) >> The issue here is that the sequences I,m indexing are not generated by >> the >> NCBI nor stored there...although I belive you´re just refering to the >> tool >> itself and not to a retrieval from the NCBI. >> >> Thanks again you´re all great giving advice to newbies like me ;) >> >> Best wishes to you all >> >> >> El Jue, 5 de Noviembre de 2009, 17:02, Hotz, Hans-Rudolf escribió: >> >>> >>> Jluis >>> >>> >>>> -Then I´ll beg you to take a look at my scripts, because I don´t seem >>>> to >>>> catch the bug... >>>> >>> you haven't attached/included any scripts, have you? >>> >>> >>> Anyway, have you considered using BLAST indices (created with the >>> additional >>> flag "-o") together with the tool 'fastacmd' (which also included in >>> the >>> NCBI blast binaries) as a simple (and very fast) alternative for >>> fetching >>> sequences. >>> >>> >>> Regards, Hans >>> >>> >>> >>> >> >> >> > > -- Dr. José Luis Lavín Trueba Dpto. de Producción Agraria Grupo de Genética y Microbiología Universidad Pública de Navarra 31006 Pamplona Navarra SPAIN _______________________________________________ Bioperl-l mailing list Bioperl-l@... http://lists.open-bio.org/mailman/listinfo/bioperl-l |
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