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realmichaelhoffert / mgeasysim

Cause simulating MG data should be easy
MIT License
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Modularize #5

Open realmichaelhoffert opened 2 hours ago

realmichaelhoffert commented 2 hours ago

The code that actually calls the read simulator should be modularized into its own function, which down the line could allow the function to accept various read simulating tools. simulate.py lines 75-80

            # simulate reads
            outfile = f'{BASE_PATH}/sim{sim}/fqs/{row['index']}'
            if not os.path.exists(f'{outfile}_R1.fq.gz'):
                command1 = f'art_illumina -ss HS25 -i {file} -l 150 -f {fold_coverage} -d {row['index']} -m 300 -s 5 -o {outfile}_R -p'
                command2 = f'gzip {outfile}_R*'
                read_simulations.append(f'{command1} && {command2}')
                logger.info(f'Added command: {command1} && {command2}')
            else:
                logger.info(f'File already exists: {outfile}_R1.fq.gz')
                already_exists += 1
realmichaelhoffert commented 2 hours ago

Would also require some additional arguments in the simulate argparser