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). Also, the indexes are smaller in size than the sequence file...
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 >
