--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/filter_by_fasta_ids.py	Fri Sep 26 14:23:16 2014 -0400
@@ -0,0 +1,113 @@
+#!/usr/bin/env python
+""" A script to build specific fasta databases """
+from __future__ import print_function
+import sys
+import logging
+
+#===================================== 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])
+
+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 target_match(target, search_entry):
+    ''' Matches '''
+    search_entry = search_entry.upper()
+    for atarget in target:
+        if search_entry.find(atarget) > -1:
+            return atarget
+    return None
+
+
+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}
+    targets = []
+
+    f_target = open(sys.argv[1])
+    for line in f_target.readlines():
+        targets.append(">%s" % line.strip().upper())
+    f_target.close()
+
+    logging.info('Read target file and am now looking for %d %s', len(targets), 'sequences.')
+
+    work_summary['wanted'] = len(targets)
+    homd_db = FASTAReader(sys.argv[2])
+
+    i = 0
+    output = open(sys.argv[3], "w")
+    try:
+        for entry in homd_db:
+            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()
+                if sequence in used_sequences:
+                    work_summary['duplicates'] += 1
+                else:
+                    used_sequences.add(sequence)
+                    print(entry.header, file=output)
+                    print(sequence, file=output)
+    finally:
+        output.close()
+
+    logging.info('Completed filtering')
+    for parm, count in work_summary.items():
+        logging.info('%s ==> %d', parm, count)
+
+if __name__ == "__main__":
+    main()