Scripts for the Databases in the Proteomics Unit of CNIC

Requirements:

Python3 and the following Python packages:

• sys
• os
• logging
• urllib.request
• datetime
• re
• zipfile
• json
• from Bio import SwissProt
• from Bio import SeqIO
• from Bio.KEGG import REST
• from Bio.KEGG import Enzyme

Executions

The following scripts, download the FASTA sequences from UniProt proteomes and create the system biology database for the given species:

python src/create_db_sb.py -s human   -o databases -vv  &> logs/create_db_sb.human.log
python src/create_db_sb.py -s mouse   -o databases -vv  &> logs/create_db_sb.mouse.log
python src/create_db_sb.py -s pig     -o databases -vv  &> logs/create_db_sb.pig.log
python src/create_db_sb.py -s rabbit  -o databases -vv  &> logs/create_db_sb.rabbit.log

Create the system biology database from the given FASTA sequence:

python src/create_db_sb.py -s human   -i test/test.fa  -o test/human -vv 
python src/create_db_sb.py -s human   -i test/test.fa  -r '[^\|]*\|([^\|]*)\|' -o test/human -vv 

Add into the crontab

crontab crontab/crontab_db_sb.sh

DecoyPYrat.v2 - Fast Hybrid Decoy Sequence Database Creation for Proteomic Mass Spectromtery Analyses

Improvement on DecoyPYrat script from Sanger (https://www.sanger.ac.uk/science/tools/decoypyrat)

Execution

python src/decoyPYrat.v2.py  --output_fasta test/uniprot_MusMusculus_dic2016.decoy.fasta  --decoy_prefix=DECOY test/uniprot_MusMusculus_dic2016.fasta

cat uniprot_MusMusculus_dic2016.target.fa uniprot_MusMusculus_dic2016.decoy.fasta > uniprot_MusMusculus_dic2016.target-decoy.fa