Hi Andreas, Thanks for you work. I answer your questions as bellow:
- some small fixes: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/metaphlan2/trunk/debian/patches/fix_sequence.patch?view=markup -> fixed - some spelling issues https://anonscm.debian. org/viewvc/debian-med/trunk/packages/metaphlan2/trunk/debian/patches/spelling.patch?view=markup - 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 - 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 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. Thanks, Tin On Wed, Aug 3, 2016 at 3:38 PM Andreas Tille <[email protected]> wrote: > Hi Nicola, > > thanks for your answer. > > On Tue, Aug 02, 2016 at 04:32:31PM +0000, Nicola Segata wrote: > > Hi Andreas, > > sorry for the delay in replying. I did get your last two emails but it > > seems the fist one (On Mon, Jul 25, 2016 at 09:45:57PM) never arrived. > > Hmmm, sad that there seems to be some mail loss. > > > 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). > > > > 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?) > > Anything that qualifies as source would be really welcome. If the > generation of the binary from this source does not make a big effort (in > terms of "takes way longer than 1 hour on a decent build machine") > generating the binaries would be really prefered. > > > For the LEfSe package I just added the license in the bitbucket > repository. > > For the description, I think you can use the following page: > > https://bitbucket.org/biobakery/biobakery/wiki/lefse > > Does it sound like an appropriate description for the package? > > I found this after I've sent my mails - thanks for confirming that this > is the correct description. I've just uploaded the package to the > Debian new queue. > > > Let me know if you have other questions or if I missed answering to other > > emails. > > If Tin will answer the binary data issue above I have no further > questions and do not remember any unanswered e-mails. > > > thanks so much for your work! > > You are welcome > > Andreas. > > -- > http://fam-tille.de >
