jpayne@0: #! /usr/bin/env python3.6
jpayne@0: 
jpayne@0: import argparse
jpayne@0: import uuid
jpayne@0: import os, sys
jpayne@0: from os.path import join as j
jpayne@0: from itertools import zip_longest
jpayne@0: 
jpayne@0: def setup(base_dir, names=[], fwds=[], revs=[], extension='fastq', pattern="{name}.{orient}.{ext}"):
jpayne@0: 	if fwds and revs and names and len(fwds) != len(revs) != len(names):
jpayne@0: 		raise ValueError('number of forward reads must equal number of reverse reads and names')
jpayne@0: 	elif len(fwds) != len(names) or not fwds or not names:
jpayne@0: 		raise ValueError('number of forward reads must equal number of names')
jpayne@0: 	with open(j(base_dir, 'snp-unwind.sh'), 'w') as unwind:
jpayne@0: 		#dir = j(base_dir, str(uuid.uuid4()))
jpayne@0: 		for i, (name, fwd, rev) in enumerate(zip_longest(names, fwds, revs)):
jpayne@0: 			dir = j(base_dir, str(i))
jpayne@0: 			sample_dir = j(dir, name)
jpayne@0: 			os.makedirs(sample_dir)
jpayne@0: 			target_f = j(sample_dir, pattern.format(name=name, orient=1, ext=extension))
jpayne@0: 			if rev:
jpayne@0: 				target_r = j(sample_dir, pattern.format(name=name, orient=2, ext=extension))
jpayne@0: 			os.symlink(fwd, target_f)
jpayne@0: 			if rev:
jpayne@0: 				os.symlink(rev, target_r)
jpayne@0: 			print(sample_dir)
jpayne@0: 			if rev:
jpayne@0: 				unwind.write('unlink {}\n'.format(target_r))
jpayne@0: 			unwind.write('unlink {}\n'.format(target_f))
jpayne@0: 			unwind.write('rmdir {}\n'.format(sample_dir))
jpayne@0: 		unwind.write('rmdir {}\n'.format(dir))
jpayne@0: 			
jpayne@0: 	
jpayne@0: 	
jpayne@0: 
jpayne@0: if __name__ == '__main__':
jpayne@0: 	parser = argparse.ArgumentParser(description="set up fastq symlink directories for snp-pipeline")
jpayne@0: 	parser.add_argument('base_dir')
jpayne@0: 	parser.add_argument('-n', dest='names', type=str, action='append', default=[])
jpayne@0: 	parser.add_argument('-f', dest='fwds', type=str, action='append', default=[])
jpayne@0: 	parser.add_argument('-r', dest='revs', type=str, action='append', default=[])
jpayne@0: 	parser.add_argument('-e', dest='extension', default='fastq')
jpayne@0: 	parser.add_argument('-p', dest='pattern', default='{name}.{orient}.{ext}')
jpayne@0: 	params = parser.parse_args()
jpayne@0: 	setup(**vars(params))