--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter_by_fasta_ids.py	Tue May 24 13:05:22 2016 -0400
@@ -0,0 +1,100 @@
+#!/usr/bin/env python
+""" A script to build specific fasta databases """
+from __future__ import print_function
+import optparse
+
+
+# ===================================== 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 '''
+        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] != '>':
+            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'''
+
+    parser = optparse.OptionParser()
+    parser.add_option('--dedup', dest='dedup', action='store_true', default=False, help='Whether to remove duplicate sequences')
+    (options, args) = parser.parse_args()
+
+    targets = []
+
+    with open(args[0]) as f_target:
+        for line in f_target.readlines():
+            targets.append(">%s" % line.strip().upper())
+
+    print('Read target file, now looking for %d sequences.' % len(targets))
+
+    work_summary = {'wanted': len(targets), 'found': 0}
+    if options.dedup:
+        used_sequences = set()
+        work_summary['duplicates'] = 0
+    homd_db = FASTAReader(args[1])
+
+    with open(args[2], "w") as output:
+        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 options.dedup:
+                    if sequence in used_sequences:
+                        work_summary['duplicates'] += 1
+                        continue
+                    else:
+                        used_sequences.add(sequence)
+                print(entry.header, file=output)
+                print(sequence, file=output)
+
+    print('Completed filtering.')
+    for parm, count in work_summary.items():
+        print('%s ==> %d' % (parm, count))
+
+if __name__ == "__main__":
+    main()