Hi Andreas, If you can use the latest version with the name changes as I mentioned, it would fit better with the updated tutorial on the metaphlan2 repository.
Thanks, Tin On Thu, Aug 4, 2016 at 1:28 PM Nicola Segata <[email protected]> wrote: > Hi Andreas, > yes, it is likely that the code will be frequently updated, but the big > database file will change only rarely (for sure no more frequently than > once a year). > thanks > Nicola > > On Thu, Aug 4, 2016 at 12:46 PM Andreas Tille <[email protected]> wrote: > >> Hi again, >> >> On Thu, Aug 04, 2016 at 08:10:29AM +0000, Nicola Segata wrote: >> > Makes sense to me! >> >> https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=833388#15 >> >> If you read the discussion it seems that my suggestion to ship the fasta >> file inside the Debian package and let the postinst do the >> transformation step found some agreement - provided that there are no >> frequent changes in the package and several uploads per month will >> happen. >> >> I'm now wondering what your estimated change rate for the metaphlan2 >> data files might be. Do these change frequently? Is there any chance >> that the code changes frequently but the data files stay unchanged? >> >> Kind regards >> >> Andreas. >> >> > 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 >> > > >> >> -- >> http://fam-tille.de >> >
