analysis-windows.py: change the size of windows in a .analysis file produced by Vidjil

This could be helpful when changing the default window size to handle the existing .analysis files.
Ideally, we should use the same library than fuse.py, but currently only the .vidjil files are recognized by the former.

tools/analysis-windows.py

+
+import json
+import argparse
+
+parser = argparse.ArgumentParser(description = 'Change the window in "id" fields within .analysis files\nTo be used for maintenance purposes only')
+parser.add_argument('--window', '-w', type=int, default=50, help='new window length (%default)')
+parser.add_argument('--overwrite', '-o', action='store_true', help='overwrite existing .analysis files')
+parser.add_argument('file', nargs='+', help='''.vidjil files''')
+
+args = parser.parse_args()
+
+def change_window(clone, w):
+    old_window = clone['id']
+    pos = clone['sequence'].find(old_window)
+
+    if pos < 0:
+        print("! Clone without window in 'id' - clone '%s' unchanged" % old_window)
+        return
+
+    new_start = pos + (len(old_window) - w) / 2
+
+    if new_start < 0 or new_start+w > len(clone['sequence']):
+        print("! Sequence too short for new window - clone '%s' unchanged" % old_window)
+        return
+
+    new_window = clone['sequence'][new_start:new_start+w]
+
+    clone['id'] = new_window
+
+
+
+class Analysis():
+
+    def __init__(self):
+        self.d = {}
+
+    def load(self, f):
+        self.d = json.load(f)
+
+    def save(self, f):
+        json.dump(self.d, f, indent=2)
+
+    def __iter__(self):
+        '''Iter on clones'''
+        return self.d["clones"].__iter__()
+            
+
+
+suffix = '' if args.overwrite else '.new'
+    
+for f in args.file:
+    f_new = f + suffix
+    print("  %s ==> %s" % (f, f_new))
+    
+    an = Analysis()
+    
+    with open(f) as ff:
+        an.load(ff)
+    
+    for clone in an:
+        change_window(clone, args.window)
+
+    with open(f_new, 'w') as ff_new:
+        an.save(ff_new)