--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/COPYING	Fri Sep 26 14:23:16 2014 -0400
@@ -0,0 +1,121 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Fri Sep 26 14:23:16 2014 -0400
@@ -0,0 +1,47 @@
+GalaxyP - Filter by FASTA IDs
+=============================
+
+* Home: <https://bitbucket.org/galaxyp/filter_by_fasta_ids>
+* Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/filter_by_fasta_ids>
+* Tool ID: `filter_by_fasta_ids`
+
+
+Description
+-----------
+
+Extract sequences from a FASTA file based on a list of IDs.
+
+
+GalaxyP Community
+-----------------
+
+Current governing community policies for [GalaxyP](https://bitbucket.org/galaxyp/) and other information can be found at:
+
+<https://bitbucket.org/galaxyp/galaxyp>
+
+
+License
+-------
+
+Copyright (c) 2014 Regents of the University of Minnesota and Authors listed below.
+
+To the extent possible under law, the author(s) have dedicated all copyright and related and neighboring rights to this software to the public domain worldwide. This software is distributed without any warranty.
+
+You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see <https://creativecommons.org/publicdomain/zero/1.0/>.
+
+You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission.
+
+
+Contributing
+------------
+
+Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://bitbucket.org/galaxyp/galaxyp/CONTRIBUTORS.md> unless you opt-out.
+
+
+Authors
+-------
+
+Authors and contributors:
+
+* John Chilton <jmchilton@gmail.com>
+* Minnesota Supercomputing Institute, Univeristy of Minnesota

--- /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()

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/filter_by_fasta_ids.xml	Fri Sep 26 14:23:16 2014 -0400
@@ -0,0 +1,13 @@
+<tool id="filter_by_fasta_ids" version="1.0" name="Filter by FASTA IDs">
+  <description>Extract sequences from a FASTA file based on a list of IDs</description>
+  <command interpreter="python">filter_by_fasta_ids.py $identifiers $input $output</command>
+  <inputs>
+    <param format="fasta" name="input" type="data" label="FASTA sequences"/>
+    <param format="txt" name="identifiers" type="data" label="List of IDs to extract sequences for"/>
+  </inputs>
+  <outputs>
+    <data format="fasta" name="output" label="FASTA sequences for ${identifiers.name}"/>
+  </outputs>
+  <help>
+  </help>
+</tool>