ParkinsonLab/MetaPro

Config.ini

Closed this issue · 4 comments

Jeltje commented

I'm attempting to create my own Config.ini based on the example in this repo, and the following aren't obvious to me:

Host: %(database_path)s/human_cds/Human_cds.fasta # this file was not downloaded with lib_downloader.py and I don't see it at https://compsysbio.org/metapro_libs/. Where do I find it?

DNA_DB: %(database_path)s/ChocoPhlAn/ChocoPhlAn.fasta I have chocophlan_h3_chunks fasta files, but they're numbered chocophlan_chunk_0.fasta, chocophlan_chunk_1.fasta, etc. How do I set DNA_DB ?

DNA_DB_Split: %(database_path)s/ChocoPhlAn/ChocoPhlAn_split/ is now chocophlan_h3_unique ?

Jeltje commented

I've also never seen %(database_path)s as a variable name, is this correct?

billytaj commented

  1. host files whatever the user wants to use. Here, we used coding sequences, but it's completely up to the user. It should work with any fasta file. We're actually exploring the efficacy of using different files to filter for contaminants.

  2. Yes, that's a variable name. The config file is parsed using Python's ConfigParser library, and this is an acceptable convention to do it.

Jeltje commented

Thanks.
Since the downloader creates every other necessary file maybe it's useful to default-download your standard recommendation (ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/current_human)? After all, adapters can also be unique to the user but you provide some anyway.

billytaj commented

noted.