--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snp-wind.py	Wed Jan 24 14:18:21 2018 -0500
@@ -0,0 +1,45 @@
+#! /usr/bin/env python3.6
+
+import argparse
+import uuid
+import os, sys
+from os.path import join as j
+from itertools import zip_longest
+
+def setup(base_dir, names=[], fwds=[], revs=[], extension='fastq', pattern="{name}.{orient}.{ext}"):
+	if fwds and revs and names and len(fwds) != len(revs) != len(names):
+		raise ValueError('number of forward reads must equal number of reverse reads and names')
+	elif len(fwds) != len(names) or not fwds or not names:
+		raise ValueError('number of forward reads must equal number of names')
+	with open(j(base_dir, 'snp-unwind.sh'), 'w') as unwind:
+		#dir = j(base_dir, str(uuid.uuid4()))
+		for i, (name, fwd, rev) in enumerate(zip_longest(names, fwds, revs)):
+			dir = j(base_dir, str(i))
+			sample_dir = j(dir, name)
+			os.makedirs(sample_dir)
+			target_f = j(sample_dir, pattern.format(name=name, orient=1, ext=extension))
+			if rev:
+				target_r = j(sample_dir, pattern.format(name=name, orient=2, ext=extension))
+			os.symlink(fwd, target_f)
+			if rev:
+				os.symlink(rev, target_r)
+			print(sample_dir)
+			if rev:
+				unwind.write('unlink {}\n'.format(target_r))
+			unwind.write('unlink {}\n'.format(target_f))
+			unwind.write('rmdir {}\n'.format(sample_dir))
+		unwind.write('rmdir {}\n'.format(dir))
+			
+	
+	
+
+if __name__ == '__main__':
+	parser = argparse.ArgumentParser(description="set up fastq symlink directories for snp-pipeline")
+	parser.add_argument('base_dir')
+	parser.add_argument('-n', dest='names', type=str, action='append', default=[])
+	parser.add_argument('-f', dest='fwds', type=str, action='append', default=[])
+	parser.add_argument('-r', dest='revs', type=str, action='append', default=[])
+	parser.add_argument('-e', dest='extension', default='fastq')
+	parser.add_argument('-p', dest='pattern', default='{name}.{orient}.{ext}')
+	params = parser.parse_args()
+	setup(**vars(params))
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