INNER CODE UNIT · Python

main

TobyBaril/EarlGrey · scripts/extract_align.py:112

def main():	
##Get input arguments
	GENOMEFA, BLAST, LIB, LBUFFER, RBUFFER, HITNUM, ALIGN, TRIMAL, EMBOSS, LOG = get_args()

# Setup logging and script timing
	handlers = [logging.FileHandler('extract_align.log'), logging.StreamHandler()]
	logging.basicConfig(format='', handlers = handlers)
	logging.getLogger().setLevel(getattr(logging, LOG.upper()))

	start_time = time.time()

	LOGGER.info('#\n# extract_align.py\n#')

	LOGGER.info('Genome file: ' + GENOMEFA)
	LOGGER.info('Blast file: ' + BLAST)
	LOGGER.info('TE library: ' + LIB)
	LOGGER.info('Left buffer size: ' + str(LBUFFER))
	LOGGER.info('Right buffer size: ' + str(RBUFFER))

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