Merge branch 'master' of github.com:bl0b/scriptsforb

bl0b · Jul 20, 2013 · 0e9adaa · 0e9adaa
2 parents 56459d9 + 1e34830
commit 0e9adaa
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Showing 2 changed files with 9 additions and 5 deletions.
diff --git a/convert_exonerate_to_fasta.py b/convert_exonerate_to_fasta.py
@@ -15,18 +15,22 @@
 if args[0] == '-s':
     args = args[1:]
     pred_a = lambda x: x != '#'
+    ts_remove = set(['.', 'a', 'c', 't', 'g', '{', '}'])
+    pred_ts = lambda x: x not in ts_remove
+    suffix = '_STRIPPED'
 else:
     pred_a = lambda x: True
+    suffix = ''
 
 
 for filename in args:
     e = Exonerate(filename)
-    out = open(filename + '.fas', 'w')
+    out = open(filename + suffix + '.fas', 'w')
     for q in e.queries:
         tseq = ''.join(ts
                        for qp, tp, ts, a
-                        in q.iterate(pred_a=pred_a))
+                        in q.iterate(pred_a=pred_a, pred_ts=pred_ts))
         s = Sequence(q.Query.split(' ')[0] + '_' + q.Target
-                     + ('#' in q.alignment and '_STRIPPED' or ''),
+                     + ('#' in q.alignment and suffix or ''),
                      tseq.replace('-', 'N'))
         print >> out, s
diff --git a/parse_exonerate.py b/parse_exonerate.py
@@ -151,12 +151,12 @@ def _rd_q(self, l):
 
     def _rd_al(self, l):
         #print "read alignment", l.strip()
-        self.alignment += l[8:]
+        self.alignment += l[8:-1]
         return True
 
     def _rd_tgt(self, l):
         #print "read target", l.strip()
-        self.target_prot += l[8:]
+        self.target_prot += l[8:-1]
         return True
 
     def _rd_dna(self, l):