--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/aragorn_out_to_gff3.py	Thu Jan 22 13:15:51 2015 -0500
@@ -0,0 +1,165 @@
+#!/usr/bin/env python
+import re
+
+def start_pattern(string):
+    return re.match(r'^[0-9]+\.$', string) \
+        or string.startswith('Number of possible') \
+        or string.startswith('Searching for')
+
+def blank_line(string):
+    return re.match(r'^\s*$', string)
+
+def blocks(iterable):
+    accumulator = []
+    run_of_blanklines = 0
+    for line in iterable:
+        # Count blank lines
+        if blank_line(line):
+            run_of_blanklines += 1
+        else:
+            run_of_blanklines = 0
+
+        if start_pattern(line) or run_of_blanklines > 2 or 'Mean G+C' in line:
+            if accumulator:
+                yield accumulator
+                accumulator = [line]
+        else:
+            accumulator.append(line)
+    if accumulator:
+        yield accumulator
+
+IMPORTANT_INFO = {
+    'trna': re.compile(r'tRNA-(?P<codon>[A-Za-z]{3})\((?P<anticodon>[A-Za-z]{3})\)'),
+    'trna-alt': re.compile(r'tRNA-\?\((?P<codon>[^\)]+)\)\((?P<anticodon>[A-Za-z]{2,})\)'),
+    'bases': re.compile(r'(?P<bases>[0-9]+) bases, %GC = (?P<gc>[0-9.]+)'),
+    'sequence': re.compile(r'Sequence (?P<complement>[c]{0,1})\[(?P<start>\d+),(?P<end>\d+)\]'),
+    'possible_pseudogene': re.compile(r'(?P<pseudo>Possible Pseudogene)'),
+}
+INFO_GROUPS = ('codon', 'anticodon', 'bases', 'gc', 'complement', 'start', 'end', 'pseudo')
+
+def important_info(block):
+    info = {}
+    for line in block:
+        for matcher in IMPORTANT_INFO:
+            matches = IMPORTANT_INFO[matcher].search(line)
+            if matches:
+                for group in INFO_GROUPS:
+                    try:
+                        info[group] = matches.group(group)
+                    except:
+                        pass
+    return info
+
+IMPORTANT_INFO_TMRNA = {
+    'tag_peptide': re.compile(r'Tag peptide:\s+(?P<pep>[A-Z*]*)'),
+    'location': re.compile(r'Location (?P<complement>[c]{0,1})\[(?P<start>\d+),(?P<end>\d+)\]'),
+}
+INFO_GROUPS_TMRNA = ('start', 'end', 'pep')
+
+def important_info_tmrna(block):
+    info = {}
+    for line in block:
+        for matcher in IMPORTANT_INFO_TMRNA:
+            matches = IMPORTANT_INFO_TMRNA[matcher].search(line)
+            if matches:
+                for group in INFO_GROUPS_TMRNA:
+                    try:
+                        info[group] = matches.group(group)
+                    except:
+                        pass
+    return info
+
+import fileinput
+stdin_data = []
+for line in fileinput.input():
+    stdin_data.append(line)
+
+possible_blocks = [line for line in blocks(stdin_data)]
+
+seqid = None
+print '##gff-version-3'
+# We're off to a GREAT start, if I'm accessing by index you just know that I'm going to do terrible
+# awful things
+for block_idx in range(len(possible_blocks)):
+    block = possible_blocks[block_idx]
+    data = None
+    fasta_defline = None
+
+    if block[0].startswith('Searching for') or 'nucleotides in sequence' in block[-1]:
+        # Try and get a sequence ID out of it
+        try:
+            fasta_defline = block[-2].strip()
+        except:
+            # Failing that, ignore it.
+            pass
+    else:
+        # They DUPLICATE results in multiple places, including a fasta version
+        # in the 'full report'.
+        possible_ugliness = [x for x in block if x.startswith('>t')]
+        if len(possible_ugliness) > 0:
+            continue
+
+        # However, if it didn't have one of those all important pieces of
+        # information, then it's either a different important piece of
+        # information, or complete junk
+        data = important_info(block)
+
+        # I am not proud of any of this. We essentially say "if that block
+        # didn't come up with useful info, then try making it a tmrna"
+        if len(data.keys()) == 0:
+            data = important_info_tmrna(block)
+            # And if that fails, just none it.
+            if len(data.keys()) == 0:
+                data = None
+            else:
+                # But if it didn't, confirm that we're a tmRNA
+                data['type'] = 'tmRNA'
+        else:
+            # If we did have keys, and didn't pass through any of the tmRNA
+            # checks, we're tRNA
+            data['type'] = 'tRNA'
+
+    # If we got a sequence ID in this block, set the defline
+    if 'nucleotides in sequence' in block[-1]:
+        try:
+            fasta_defline = block[-2].strip()
+        except:
+            pass
+
+    # if a defline is available, try and extract the fasta header ID
+    if fasta_defline is not None:
+        try:
+            seqid = fasta_defline[0:fasta_defline.index(' ')]
+        except:
+            seqid = fasta_defline
+
+    # If there's data
+    if data is not None and len(data.keys()) > 1:
+
+        # Deal with our flags/notes.
+        if data['type'] == 'tRNA':
+            # Are these acceptable GFF3 tags?
+            notes = {
+                'Codon': data['codon'],
+                'Anticodon': data['anticodon'],
+            }
+            if 'pseudo' in data:
+                notes['Note'] = 'Possible pseudogene'
+        else:
+            notes = {
+                'Note': 'Tag peptide: ' + data['pep'] + ''
+            }
+
+        notestr = ';'.join(['%s="%s"' % (k,v) for k,v in notes.iteritems()])
+
+        print '\t'.join([
+            seqid,
+            'aragorn',
+            data['type'],
+            data['start'],
+            data['end'],
+            '.',
+            '.',
+            '.',
+            notestr
+        ])