From f74f336b6d80eb3472a911b9da63bdd6f2d81a3e Mon Sep 17 00:00:00 2001
From: meiermark <meiermark13@gmail.com>
Date: Wed, 12 Jul 2017 17:15:42 +0200
Subject: [PATCH] bugfix: a3m.py check functions did not return True...
 never...

---
 lib/ffindex          |  2 +-
 scripts/a3m.py       | 17 ++++++++++++++---
 scripts/check_a3m.py |  9 ++++-----
 3 files changed, 19 insertions(+), 9 deletions(-)

diff --git a/lib/ffindex b/lib/ffindex
index cceb0ffb..360e4176 160000
--- a/lib/ffindex
+++ b/lib/ffindex
@@ -1 +1 @@
-Subproject commit cceb0ffb8fe532dfee04385b5b24bebf7dc68ece
+Subproject commit 360e4176ece531be34a94298c808349916d016ac
diff --git a/scripts/a3m.py b/scripts/a3m.py
index 9767869d..f6f65779 100644
--- a/scripts/a3m.py
+++ b/scripts/a3m.py
@@ -70,9 +70,12 @@ def check_and_add_annotation(self, header, sequence):
         return False
 
     def check_match_states(self, match_states):
+        if not self.nr_match_states:
+            self.nr_match_states = match_states
+
         if match_states == 0:
             raise A3MFormatError("Sequence with zero match states!")
-        elif self.nr_match_states and match_states != self.nr_match_states:
+        elif match_states != self.nr_match_states:
             raise A3MFormatError(
                 ("Sequence with diverging number "
                  "of match states ({} vs. {})!").format(
@@ -80,8 +83,7 @@ def check_match_states(self, match_states):
                     self.nr_match_states
                 )
             )
-        else:
-            self.nr_match_states = match_states
+
 
     def check_ss_conf(self, sequence):
         count_match_states = sum((c in self.VALID_SS_CONF_STATES
@@ -96,6 +98,8 @@ def check_ss_conf(self, sequence):
             raise A3MFormatError(
                 ("Undefined character(s) '{}' in predicted "
                  "secondary structure confidence!").format(invalid_states))
+        else:
+            return True
 
     def check_ss_pred(self, sequence):
         count_match_states = sum((c in self.VALID_SS_STATES
@@ -110,6 +114,8 @@ def check_ss_pred(self, sequence):
             raise A3MFormatError(
                ("Undefined character(s) '{}' in predicted "
                 "secondary structure!").format(invalid_states))
+        else:
+            return True
 
     def check_dssp(self, sequence):
         count_match_states = sum(
@@ -122,6 +128,8 @@ def check_dssp(self, sequence):
             raise A3MFormatError(
                 ("Undefined character(s) '{}' in "
                  "dssp annotation!").format(invalid_states))
+        else:
+            return True
 
     def check_sequence(self, sequence):
         count_match_states = sum((c in self.VALID_MATCH_STATES
@@ -129,6 +137,7 @@ def check_sequence(self, sequence):
                                  for c in sequence)
         self.check_match_states(count_match_states)
 
+
         invalid_states = set(sequence) - self.VALID_MATCH_STATES
         invalid_states -= self.VALID_GAP_STATES
         invalid_states -= self.VALID_INSERTION_STATES
@@ -137,6 +146,8 @@ def check_sequence(self, sequence):
             raise A3MFormatError(
                ("Undefined character(s) '{}' in "
                 "protein sequence!").format(invalid_states))
+        else:
+            return True
 
     def get_sub_sequence(self, sequence, limits):
         sub_sequence = []
diff --git a/scripts/check_a3m.py b/scripts/check_a3m.py
index 449420c6..8578312f 100755
--- a/scripts/check_a3m.py
+++ b/scripts/check_a3m.py
@@ -7,18 +7,18 @@
 
 def check_a3m(filename):
   a3m = A3M_Container()
-  
+
   if(filename.lower() == "stdin"):
     fh = sys.stdin
   else:
     fh = open(filename, "r")
-    
+
   try:
     a3m.read_a3m(fh)
   except A3MFormatError as e:
-    sys.stderr.write(e)
+    sys.stderr.write(str(e))
     exit(1)
-  
+
 
 def main():
   filename = sys.argv[1]
@@ -27,4 +27,3 @@ def main():
 
 if __name__ == "__main__":
   main()
-