CFM-ID Python Package

This package is a Python wrapper to use CFM-ID : https://cfmid.wishartlab.com

CFM-ID provides a method for accurately and efficiently identifying metabolites in spectra generated by electrospray tandem mass spectrometry (ESI-MS/MS). The program uses Competitive Fragmentation Modeling to produce a probabilistic generative model for the MS/MS fragmentation process and machine learning techniques to adapt the model parameters from data.

This package is under devopment and work only for cfm-predict of the CFM-ID version 2.0.

Install

pip install cfm-id

Usage

from cfm_id import CfmId

cfm_id = CfmId("/path/to/cfm_id/folder")
cfm_id.predict("O=C1OC(CO)C(O)=C1O")

The default output format is a list of MatchMS Spectrum, including a "merged" spectrum of the 3 energies.

You can specify the CFM-ID raw text format export with the raw_format param :

cfm_id.predict("O=C1OC(CO)C(O)=C1O", raw_format=True)

Environment variable

You can also use environment variable CFMID_PATH rather than path argument.

export CFMID_PATH=path/to/cfm_id/folder

from cfm_id import CfmId

cfm_id = CfmId()

Param and config files

By default CfmId will use param_output.log and param_config.txt files located at the root of the cfm_id folder as respectively param and config files.

You can specify anoter files location at instantiation with local path as ist of string :

from cfm_id import CfmId

cfm_id = CfmId(
    "/path/to/cfm_id/folder",
    param=["param", "param_output0_neg.log"], conf=["conf", "param_config_neg.txt"]
)

In this example, the cfm_id instance will use /path/to/cfm_id/folder/param/param_output0_neg.log as param file.

Use Docker image

You can use a Docker image for CFM-ID rather than local files by using CfmIdDocker class.

from cfm_id import CfmIdDocker

cfm_id = CfmIdDocker("myrepo/image_name:tag")

In the Docker image, cfm-predict has to be in the PATH environment variable and param_output.log and param_config.txt files must be located at the working directory.

You can also use environment variable CFMID_IMAGE rather than path argument.

export CFMID_IMAGE=myrepo/image_name:tag

from cfm_id import CfmIdDocker

cfm_id = CfmIdDocker()