computational-metabolomics / beamspy

BEAMSpy - Birmingham mEtabolite Annotation for Mass Spectrometry (Python Package)

BEAMSpy - Birmingham mEtabolite Annotation for Mass Spectrometry (Python package)

BEAMSpy (Birmingham mEtabolite Annotation for Mass Spectrometry) is a Python package that includes several automated and seamless computational modules that are applied to putatively annotate metabolites detected in untargeted ultra (high) performance liquid chromatography-mass spectrometry or untargeted direct infusion mass spectrometry metabolomic assays. All reported metabolites are annotated to level 2 or 3 of the Metabolomics Standards Initiative (MSI) reporting standards (Metabolomics. 2007 Sep; 3(3): 211–221. doi: 10.1007/s11306-007-0082-2). The package is highly flexible to suit the diversity of sample types studied and mass spectrometers applied in untargeted metabolomics studies. The user can use the standard reference files included in the package or can develop their own reference files.

• Documentation (Read the Docs)
• Bug reports

Quick installation

Conda

1. Install Miniconda. Follow the steps described here.
2. Run the following commands to install BEAMSpy.

Windows-64, Linux-64 and OSx

$ conda create -n beamspy beamspy -c conda-forge -c bioconda -c computational-metabolomics
$ activate beamspy

Linux-64 and OSx

$ conda create -n beamspy beamspy -c conda-forge -c bioconda -c computational-metabolomics
$ source activate beamspy

Usage

Command line interface (CLI)

$ beamspy --help

Graphical user interface (GUI)

$ beamspy start-gui

Bug reports

Please report any bugs that you find here. Or fork the repository on GitHub and create a pull request (PR). We welcome all contributions, and we will help you to make the PR if you are new to git.

Credits

• Team (University of Birmingham and EMBL-EBI)

Code base

• Ralf J. M. Weber ([email protected]) - University of Birmingham (UK)

License

Released under the GNU General Public License v3.0 (see LICENSE)

beamspy's Issues

TypeError: 'method' object is not subscriptable

Hi there.
I wanted to run your Jupyter NB w/ your test data, however, executing

annotate_adducts(graphs, db_out, ppm, lib_adducts)
df_out = summary(df, db_out)
print(df_out)

resulted in the following error:

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-4-5b48a2fbb04c> in <module>
----> 1 annotate_adducts(graphs, db_out, ppm, lib_adducts)
      2 df_out = summary(df, db_out)
      3 print(df_out)

c:\ProgramData\Anaconda3\lib\site-packages\beamspy\annotation.py in annotate_adducts(source, db_out, ppm, lib, add)
    394     if isinstance(source, list) and len(source) > 0 and isinstance(source[0], nx.classes.digraph.DiGraph):
    395         for i, graph in enumerate(source):
--> 396             for assignment in _annotate_pairs_from_graph(graph, lib_pairs=lib_pairs, ppm=ppm, charge=None):
    397                 cursor.execute("""INSERT OR REPLACE into adduct_pairs (peak_id_a, peak_id_b, 
    398                                label_a, label_b,

c:\ProgramData\Anaconda3\lib\site-packages\beamspy\annotation.py in _annotate_pairs_from_graph(G, ppm, lib_pairs, charge)
    167     for e in G.edges(data=True):
    168 
--> 169         mz_x = G.nodes[e[0]]["mz"]
    170         mz_y = G.nodes[e[1]]["mz"]
    171 

TypeError: 'method' object is not subscriptable

Help is appreciated.

Cheers,
Thomas