motif_annotation

Annotate ms2lda motifs using MAGMa

Dependencies

python2
sqlalchemy
magma (see installation instructions)
rdkit (will be installed for magma)

Install / Run annotate_docs.py

git clone https://github.com/iomega/motif_annotation.git
git clone https://github.com/sdrogers/ms2ldaviz.git

motif_annotation/annotate_docs.py 190 exp190.db spectra_massbank/
>exp190_magma_annotation.json

motif_annotation/annotate_docs.py -m 1 -l MGF -a '{"name_field": "spectrumid", "min_ms2_intensity": 500}' -b 0.005 -n name 1268 exp1268.db MIADB_200_metadata.mgf >exp1268_magma_annotation.json

motif_annotation/annotate_docs.py -m 1 -q 0.1 -l MGF -a '{"name_field": "title", "min_ms2_intensity": 100}' -b 0.1 -n name 1271 exp1271.db 200323_Full_LDB_POS_02_annotated.mgf >exp1271_annotated.json

Or run using Docker:

sudo docker run -v $PWD:/data ms2lda/annotate_docs 190 data/exp190.db data/spectra_massbank/
>magma_annotation.json