sugarcaneMapperIDs

The goal of this app is the following: given a DNA or protein sequence from sugarcane map it to a desired database (from sequences in Conekt Grasses) and return the corresponding identifier used to compute expression profiles or co-expression networks.

Required software

mkdir sugarcaneMapperIDs
cd sugarcaneMapperIDs
python3 -m venv .venv
. .venv/bin/activate
pip install flask
pip install peewee
pip install biopython

Installing DB schema

The schema is available as SQL, and can be used to initialized the database in the following way:

cat db/schema.sql | sqlite3 sugarcaneSequences.db

The model.py also knows how to implement the schema, and the preferred way to initialize the database is the following:

python3 db/model.py

Populating DB

python3 utils/populate.py --cds FILES_PANTRANSCRIPTOME/all_CDS_idsok.fasta --proteins FILES_PANTRANSCRIPTOME/PanTranscriptome_2023.proteins --transcripts FILES_PANTRANSCRIPTOME/all_transcripts_checked_with_cds.fasta --orthogroup_members FILES_PANTRANSCRIPTOME/Orthogroups_panTABLE.tsv --orthogroup_representative FILES_PANTRANSCRIPTOME/transcripts_of_longest_cds_per_OG.ids