Don't filter for GC content when pruning. Leave to previous

freebarcodes/prune.py

@@ -32,16 +32,12 @@ def is_good_seq(seq):
 
 def make_iterator(raw_fpath):
     bc_list = [line.strip() for line in open(raw_fpath)]
+    bc_list.sort()
     bc_len = len(bc_list[0])
     assert all(len(bc) == bc_len for bc in bc_list), set(map(len, bc_list))
-    GC_max = min(list(range(bc_len)), key=lambda x: abs(float(x)/bc_len-0.6))
-    is_good_seq = make_is_good_seq(bc_len - GC_max, GC_max)
 
     log.info('Barcode length: {}'.format(bc_len))
-    log.info('AT/GC max: {}'.format(GC_max))
     log.info('Starting list size: {}'.format(len(bc_list)))
-    bc_list = [bc for bc in bc_list if is_good_seq(bc)]
-    log.info('Sequences after initial filtering: {}'.format(len(bc_list)))
     def iterate_good_barcodes():
         for seq in bc_list:
             yield seqtools.dna2num(seq)