From Michael.Muratet at operon.com Wed Dec 27 17:52:03 2006 From: Michael.Muratet at operon.com (Michael Muratet US-Huntsville) Date: Wed, 27 Dec 2006 16:52:03 -0600 Subject: [Bioperl-microarray] SOFT parsers Message-ID: Greetings There was a thread a few years ago regarding parsers for SOFT-formatted data (the format used by the NCBI/GEO database). Has anybody ever developed one that would put the data into a database or into another format? Thanks Mike From sdavis2 at mail.nih.gov Thu Dec 28 00:15:25 2006 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Thu, 28 Dec 2006 00:15:25 -0500 Subject: [Bioperl-microarray] SOFT parsers In-Reply-To: References: Message-ID: <459352ED.60604@mail.nih.gov> Michael Muratet US-Huntsville wrote: > Greetings > > There was a thread a few years ago regarding parsers for SOFT-formatted > data (the format used by the NCBI/GEO database). Has anybody ever > developed one that would put the data into a database or into another > format? > Hi, Michael. I have not written anything for perl, but I am the author of the GEOquery package for the R/Bioconductor project (http://www.bioconductor.org). It can download and parse all of the SOFT format files (sample, platform, series, and dataset) into objects in R. Once in R, you can apply pretty much any analysis method for microarray data, as most of these methods are available as Bioconductor packages. I am in the process of converting GEOquery to use the MINiML format files (XML) instead of the SOFT format. If you decide that you need to use perl, I would highly suggest that you use the MINiML format files instead of SOFT. Hope that helps. Sean From allenday at ucla.edu Thu Dec 28 18:14:05 2006 From: allenday at ucla.edu (Allen Day) Date: Thu, 28 Dec 2006 15:14:05 -0800 Subject: [Bioperl-microarray] SOFT parsers In-Reply-To: References: Message-ID: <5c24dcc30612281514vc055deek7986215bb58559a5@mail.gmail.com> Replying again to the list from my subscribed address. ---------- Hi Mike, I have a parser that does a partial GEO->MAGE-ML transform called Bio::MageIO, done in classic Bioperl *::IO style. I just checked CPAN, looks like I haven't published it yet. If you're interested in developing the library further I can package it up or put in CVS at open-bio. I've attached a tarball if you want to peruse first. There already exist some adapters for serializing MAGE-ML to a database, so once you have MAGE-ML you will be better off. -Allen On 12/27/06, Michael Muratet US-Huntsville wrote: > Greetings > > There was a thread a few years ago regarding parsers for SOFT-formatted > data (the format used by the NCBI/GEO database). Has anybody ever > developed one that would put the data into a database or into another > format? > > Thanks > > Mike > > _______________________________________________ > bioperl-microarray mailing list > bioperl-microarray at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-microarray > -------------- next part -------------- A non-text attachment was scrubbed... Name: Bio-MageIO-0.01.tar.gz Type: application/x-gzip Size: 2329 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/bioperl-microarray/attachments/20061228/083965a3/attachment.gz From Michael.Muratet at operon.com Wed Dec 27 22:52:03 2006 From: Michael.Muratet at operon.com (Michael Muratet US-Huntsville) Date: Wed, 27 Dec 2006 16:52:03 -0600 Subject: [Bioperl-microarray] SOFT parsers Message-ID: Greetings There was a thread a few years ago regarding parsers for SOFT-formatted data (the format used by the NCBI/GEO database). Has anybody ever developed one that would put the data into a database or into another format? Thanks Mike From sdavis2 at mail.nih.gov Thu Dec 28 05:15:25 2006 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Thu, 28 Dec 2006 00:15:25 -0500 Subject: [Bioperl-microarray] SOFT parsers In-Reply-To: References: Message-ID: <459352ED.60604@mail.nih.gov> Michael Muratet US-Huntsville wrote: > Greetings > > There was a thread a few years ago regarding parsers for SOFT-formatted > data (the format used by the NCBI/GEO database). Has anybody ever > developed one that would put the data into a database or into another > format? > Hi, Michael. I have not written anything for perl, but I am the author of the GEOquery package for the R/Bioconductor project (http://www.bioconductor.org). It can download and parse all of the SOFT format files (sample, platform, series, and dataset) into objects in R. Once in R, you can apply pretty much any analysis method for microarray data, as most of these methods are available as Bioconductor packages. I am in the process of converting GEOquery to use the MINiML format files (XML) instead of the SOFT format. If you decide that you need to use perl, I would highly suggest that you use the MINiML format files instead of SOFT. Hope that helps. Sean From allenday at ucla.edu Thu Dec 28 23:14:05 2006 From: allenday at ucla.edu (Allen Day) Date: Thu, 28 Dec 2006 15:14:05 -0800 Subject: [Bioperl-microarray] SOFT parsers In-Reply-To: References: Message-ID: <5c24dcc30612281514vc055deek7986215bb58559a5@mail.gmail.com> Replying again to the list from my subscribed address. ---------- Hi Mike, I have a parser that does a partial GEO->MAGE-ML transform called Bio::MageIO, done in classic Bioperl *::IO style. I just checked CPAN, looks like I haven't published it yet. If you're interested in developing the library further I can package it up or put in CVS at open-bio. I've attached a tarball if you want to peruse first. There already exist some adapters for serializing MAGE-ML to a database, so once you have MAGE-ML you will be better off. -Allen On 12/27/06, Michael Muratet US-Huntsville wrote: > Greetings > > There was a thread a few years ago regarding parsers for SOFT-formatted > data (the format used by the NCBI/GEO database). Has anybody ever > developed one that would put the data into a database or into another > format? > > Thanks > > Mike > > _______________________________________________ > bioperl-microarray mailing list > bioperl-microarray at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-microarray > -------------- next part -------------- A non-text attachment was scrubbed... Name: Bio-MageIO-0.01.tar.gz Type: application/x-gzip Size: 2329 bytes Desc: not available URL: