--- a/filter_by_fasta_ids.py	Mon Jan 09 14:26:41 2017 -0500
+++ b/filter_by_fasta_ids.py	Mon Feb 20 06:25:50 2017 -0500
@@ -2,65 +2,27 @@
 """ A script to build specific fasta databases """
 from __future__ import print_function
 
-
-import logging
+import collections
 import sys
 
-
-# ===================================== Iterator ===============================
-class Sequence:
-    ''' Holds protein sequence information '''
-    def __init__(self):
-        self.header = ""
-        self.sequence_parts = []
-
-    def get_sequence(self):
-        return "".join([line.rstrip().replace('\n', '').replace('\r', '') for line in self.sequence_parts])
+Sequence = collections.namedtuple('Sequence', ['header', 'sequence'])
 
 
-class FASTAReader:
-    """
-        FASTA db iterator. Returns a single FASTA sequence object.
-    """
-    def __init__(self, fasta_name):
-        self.fasta_file = open(fasta_name)
-        self.next_line = self.fasta_file.readline()
-
-    def __iter__(self):
-        return self
-
-    def __next__(self):
-        ''' Iteration '''
-        # while True:
-        #    line = self.fasta_file.readline()
-        #    if not line:
-        #        raise StopIteration
-        #    if line[0] == '>':
-        #        break
-        next_line = self.next_line
-        if not next_line:
-            raise StopIteration
-
-        seq = Sequence()
-        seq.header = next_line.rstrip().replace('\n', '').replace('\r', '')
-
-        next_line = self.fasta_file.readline()
-        while next_line and next_line[0] != '>':
-            # tail = self.fasta_file.tell()
-            # line = self.fasta_file.readline()
-            # if not line:
-            #   break
-            # if line[0] == '>':
-            #   self.fasta_file.seek(tail)
-            #   break
-            seq.sequence_parts.append(next_line)
-            next_line = self.fasta_file.readline()
-        self.next_line = next_line
-        return seq
-
-    # Python 2/3 compat
-    next = __next__
-# ==============================================================================
+def FASTAReader_gen(fasta_filename):
+    fasta_file = open(fasta_filename)
+    line = fasta_file.readline()
+    while True:
+        if not line:
+            return
+        assert line.startswith('>'), "FASTA headers must start with >"
+        header = line.rstrip()
+        sequence_parts = []
+        line = fasta_file.readline()
+        while line and line[0] != '>':
+            sequence_parts.append(line.rstrip())
+            line = fasta_file.readline()
+        sequence = "".join(sequence_parts)
+        yield Sequence(header, sequence)
 
 
 def target_match(target, search_entry):
@@ -74,9 +36,6 @@
 
 def main():
     ''' the main function'''
-    logging.basicConfig(filename='filter_fasta_log',
-                        level=logging.INFO,
-                        format='%(asctime)s :: %(levelname)s :: %(message)s',)
 
     used_sequences = set()
     work_summary = {'wanted': 0, 'found': 0, 'duplicates': 0}
@@ -87,20 +46,17 @@
             targets.append(">%s" % line.strip().upper())
 
     work_summary['wanted'] = len(targets)
-    homd_db = FASTAReader(sys.argv[2])
 
     # output = open(sys.argv[3], "w")
-    for entry in homd_db:
+    for entry in FASTAReader_gen(sys.argv[2]):
         target_matched_results = target_match(targets, entry.header)
         if target_matched_results:
             work_summary['found'] += 1
             targets.remove(target_matched_results)
-            sequence = entry.get_sequence()
+            sequence = entry.sequence
             used_sequences.add(sequence)
             print(entry.header)
             print(sequence)
-    for parm, count in work_summary.items():
-        logging.info('%s ==> %d', parm, count)
 
 
 if __name__ == "__main__":