Running MetaPathways

Input

MetaPathways inputs are fasta files provided in an input folder. The file names must end with a .fasta or .fas. These fasta files contains the contigs or DNA sequences from assembling.

Parameter File

The parameter file must indicate the setting for any MetaPathways run. An example paramter file can be downloaded as

$ wget  https://github.com/kishori82/MetaPathways_Python.3.0/raw/kmk-develop/data/text/template_param.txt

Below we describe the settings in the parameter file.

Run

As an illustration we donwload a small input file testsample1.fasta in a folder named mp_input and we want the output in a folder names mp_output

$ mkdir mp_input
$ cd mp_input
$ wget https://github.com/kishori82/MetaPathways_Python.3.0/raw/kmk-develop/data/testdata/testsample1.fasta
$ cd ..

Now we kick off a run as

$ MetaPathways --input mp_input --output mp_output -p template_param.txt -d ~/MetaPathways_DBs/