INNER CODE UNIT · Python

COUNTER

TobyBaril/EarlGrey · scripts/extract_align.py:179

			COUNTER = COUNTER + 1

##Generate new consensus with emboss if flagged
	if EMBOSS == 'y':
		for FILE in os.listdir('muscle'):
			CONSENSUSGEN(FILE)
			
##Remove empty tmp directories and unneeded files
	LOGGER.info('Removing tmp directories and extraneous files')
	shutil.rmtree('tmpbedfiles/')
	shutil.rmtree('tmpextracts/')
	shutil.rmtree('tmpTEfiles/')
	#FILES = [F for F in os.listdir('muscle/') if F.endswith('_cons.fa')]
	#for FILE in FILES:
	#	os.remove('muscle/' + FILE)
	#FILES = [F for F in os.listdir('muscle/') if F.endswith('_trimal.fa')]
	#for FILE in FILES:
	#	os.remove('muscle/' + FILE)

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