Makes sense to me! thanks Nicola On Thu, Aug 4, 2016 at 8:18 AM Andreas Tille <[email protected]> wrote:
> Hi Nicola, > > On Wed, Aug 03, 2016 at 08:51:33PM +0000, Nicola Segata wrote: > > Great, thanks Andreas. We provide the "*.bt2" files so that the user can > > run BowTie2 internally to MetaPhlAn directly without first building the > > indexes (it will take quite a bit of time). > > Fully agreed here. > > > Also, the indexes are smaller > > in size than the sequence file... > > Hmmm, all *.bt2 files sum up to 1,124,449kB while the fasta file has > only 753081kB. Considering the better compression performance of pure > text files a compressed archive containing the fasta is drastically > smaller than one with the *.bt2 files. Yesterday I tried to start a > discussion how to deal with the size of the data inside Debian[1] (no > answer so far) and my experiment to create a source tarball just > containing the fasta resulted in a 270MB *xz* compressed file (well xz > is better than gz but lets say the compressed tarball with the fasta is > about 30% of size of your current download of 1.017MB. > > The situation for Debian is different than from your users: A user who > downloads from your website intends to run metaphlan2. Amongst the > millions of Debian users only very few are interested in metaphlan2 and > we need to outweight how much resources we could spent. Its not that > only Debian provides resources. There is a large mirroring network that > spents lots of bandwidth and disk space for a very small usage. So in > this case it makes sense to put the effort on the users side to > regenerate the indexes (or even download the data separately via a > script we could provide inside the package). So I could imagine to > package only the metaphlan2 code and provide a script that downloads the > data and puts them into the expected place. > > Kind regards > > Andreas. > > [1] > https://lists.alioth.debian.org/pipermail/debian-med-packaging/2016-August/044984.html > > > cheers > > Nicola > > > > On Wed, Aug 3, 2016 at 6:08 PM Andreas Tille <[email protected]> wrote: > > > > > Hi Tin, > > > > > > On Wed, Aug 03, 2016 at 02:01:01PM +0000, Duy Tin Truong wrote: > > > > > - Tin can also provide more info about the binary data in db_v20. > The > > > files > > > > > ending with "bt2" are created using a script in the Bowtie2 package > > > > > (bowtie2-build) using a sequence file Tin can provide (it can also > be > > > > > recovered from the bt2 files with bowtie2-inspect if I remember > well). > > > > As Nicola said, those files in db_v20 are created with bowtie2-build > > > > using a sequence file and you can recover the sequence file by: > > > > > > > > bowtie2-inspect metaphlan2/db_v20/mpa_v20_m200 > > metaphlan2/markers.fasta > > > > > > > > If you want to rebuild them, the command is: > > > > > > > > bowtie2-build metaphlan2/markers.fasta metaphlan2/db_v21/mpa_v21_m200 > > > > > > I can confirm that I can reproduce the files byte identical from > > > markers.fasta. Is there any reason to ship the binary form instead of > > > the fasta text file? Moreover, what is the source of the > markers.fasta? > > > Is there any related publication or so? > > > > > > > > For the mpa_v20_m200.pkl Tin can also provide the uncompressed > python > > > > > object (or he can provide a couple of lines of code to uncompress > it?) > > > > It is python dictionary and can be read as: > > > > > > > > import cPickle as pickleimport bz2 > > > > db = pickle.load(bz2.BZ2File('db_v20/mpa_v20_m200.pkl', 'r')) > > > > > > > > You can have more information about them at: > > > > > > > > https://bitbucket.org/biobakery/metaphlan2#markdown-header-customizing-the-database > > > > > > OK, that page clarifies the method. Just a personal remark from the > > > point of view of an outsider of bioinformatics: I'd regard the > creation > > > process of the mpa_v20_m200.pkl file a bit cumbersome. I'd personally > > > prefer droping some text record somewhere and call a script processing > > > this record rather than writing an own script. > > > > > > > In addition, some files were changed the names: > > > > - metaphlan2_strainer.py -> strainphlan.py > > > > - strainer_src -> strainphlan_src > > > > - strainer_tutorial -> strainphlan_tutorial > > > > > > > > Some source files were updated as well. > > > > Please let me know if you need other information. > > > > > > Just drop me a not once you might release a new version containing > these > > > changes. I think I'll try to release the current version as is since > at > > > least the origin of the files is clarified now. I'm not yet sure > whether > > > the size of the data is acceptable or might spoil some limit. > Regarding > > > this I'm wondering whether I create a source tarball including rather > > > markers.fasta and create the bt2 files in the build process. > > > > > > Kind regards > > > > > > Andreas. > > > > > > -- > > > http://fam-tille.de > > > > > -- > http://fam-tille.de >
