Hi Andreas,
Thanks for you work. I answer your questions as bellow:
-> fixed
- 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 pickle
import bz2
db = pickle.load(bz2.BZ2File('db_v20/mpa_v20_m200.pkl', 'r'))
You can have more information about them at:
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