diff snp_wind.py @ 0:201984e0cab2 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snp_wind.py	Fri Oct 13 14:20:19 2023 +0000
@@ -0,0 +1,42 @@
+#!/usr/bin/env python
+
+import argparse
+import os
+from os.path import join as j
+from itertools import zip_longest
+
+
+def setup(base_dir, names=[], fwds=[], revs=[], extension='vcf', 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:
+        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 vcf 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='vcf')
+    parser.add_argument('-p', dest='pattern', default='{name}.{orient}.{ext}')
+    params = parser.parse_args()
+    setup(**vars(params))