--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alignment/phytab_mafft.py	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,216 @@
+#!/usr/bin/env python
+
+import os
+import optparse
+import subprocess
+from multiprocessing import Pool
+
+directory = ""
+results = "results.data"
+extension = ".fs"
+aligned_extension = ".afa"
+
+
+def unescape(string):
+    mapped_chars = {
+        '>': '__gt__',
+        '<': '__lt__',
+        "'": '__sq__',
+        '"': '__dq__',
+        '[': '__ob__',
+        ']': '__cb__',
+        '{': '__oc__',
+        '}': '__cc__',
+        '@': '__at__',
+        '\n': '__cn__',
+        '\r': '__cr__',
+        '\t': '__tc__',
+        '#': '__pd__'
+        }
+
+    for key, value in mapped_chars.iteritems():
+        string = string.replace(value, key)
+
+    return string
+
+
+def isTabular(file):
+    with open(file) as f:
+        for line in f:
+            if line[0] == '>':
+                return False
+    return True
+
+
+def toData(text):
+	text = text.split('\n')
+	result = ''
+	for line in text:
+	    if '>' in line:
+	        line = '\n' + line.replace('> ', "") + '\t'
+	    line = line.replace(" ", "\t")
+	    result += line
+	return result[1:]  # Index past the first newline char
+
+def toDataSingle(text):
+	text = text.split('\n')
+	result = ''
+	for line in text:
+		line = line + '\n'
+ 		result += line
+	return result[1:]  # Index past the first newline char
+
+def mafftauto(input):
+    file_name = directory + os.sep + input
+    aln = file_name + aligned_extension
+    call = subprocess.call(['mafft', '--auto', '--out', aln, file_name])  
+
+def mafft1(input):
+    file_name = directory + os.sep + input
+    aln = file_name + aligned_extension
+    call = subprocess.call(['mafft', '--retree', '1', '--out', aln, file_name])  
+
+def mafft2(input):
+    file_name = directory + os.sep + input
+    aln = file_name + aligned_extension
+    call = subprocess.call(['mafft', '--retree', '2', '--out', aln, file_name])  
+
+def maffti(input):
+    file_name = directory + os.sep + input
+    aln = file_name + aligned_extension
+    call = subprocess.call(['mafft-fftnsi', '--out', aln, file_name])  
+
+def maffteinsi(input):
+    file_name = directory + os.sep + input
+    aln = file_name + aligned_extension
+    call = subprocess.call(['mafft-einsi', '--out', aln, file_name])  
+
+def mafftlinsi(input):
+    file_name = directory + os.sep + input
+    aln = file_name + aligned_extension
+    call = subprocess.call(['mafft-linsi', '--out', aln, file_name])  
+
+def mafftginsi(input):
+    file_name = directory + os.sep + input
+    aln = file_name + aligned_extension
+    call = subprocess.call(['mafft-ginsi', '--out', aln, file_name])  
+
+def mafftqinsi(input):
+    file_name = directory + os.sep + input
+    aln = file_name + aligned_extension
+    call = subprocess.call(['mafft-qinsi', '--out', aln, file_name])  
+
+
+class Sequence:
+    def __init__(self, string):
+        lis = string.split()
+        self.species = lis[0]
+        self.family = lis[1]
+        self.name = lis[2]
+        self.header = ' '.join(lis[:-1])
+        self.sequence = lis[-1]
+        self.string = string
+
+    def printFASTA(self):
+        return '> ' + self.header + '\n' + self.sequence + '\n'
+
+
+def saveMulti(tabFile):
+    with open(tabFile) as f:
+        for line in f:
+            seq = Sequence(line)
+            with open(directory + os.sep + seq.family + extension, "a") as p:
+                p.write(seq.printFASTA())
+
+
+def saveSingle(fastaFile):
+    with open(fastaFile) as f:
+        for line in f:
+            with open(directory + os.sep + "fasta" + extension, "a") as p:
+                p.write(line)
+
+
+def main():
+    usage = """%prog [options]
+options (listed below) default to 'None' if omitted
+    """
+    parser = optparse.OptionParser(usage=usage)
+
+    parser.add_option(
+        '-d', '--directory',
+        metavar="PATH",
+        dest='path',
+        default='.',
+        help='Path to working directory.')
+
+    parser.add_option(
+        '-i', '--in',
+        dest='input',
+        action='store',
+        type='string',
+        metavar="FILE",
+        help='Name of input data.')
+    
+    parser.add_option(
+        '-s', '--strat',
+        dest='strategy',
+        action='store',
+        type='string',
+        help='Alignement algorithm to use.')
+
+    options, args = parser.parse_args()
+
+    global directory
+    inputFile = unescape(options.input)
+    directory = unescape(options.path) + os.sep + "data"
+    strategy = unescape(options.strategy)
+    
+    os.mkdir(directory)
+
+    if isTabular(inputFile):
+        saveMulti(inputFile)
+    else:
+        saveSingle(inputFile)
+
+    pool = Pool()
+    list_of_files = [file for file in os.listdir(directory) if file.lower().endswith(extension)]
+    list_of_files = sorted(list_of_files)
+    if strategy == 'Auto':
+        pool.map(mafftauto, list_of_files)
+        
+    elif strategy == 'FFT-NS-1':
+        pool.map(mafft1, list_of_files)
+    
+    elif strategy == 'FFT-NS-2':
+        pool.map(mafft2, list_of_files)
+
+    elif strategy == 'FFT-NS-i':
+        pool.map(maffti, list_of_files)
+
+    elif strategy == 'E-INS-i':
+        pool.map(maffteinsi, list_of_files)
+
+    elif strategy == 'L-INS-i':
+        pool.map(mafftlinsi, list_of_files)
+
+    elif strategy == 'G-INS-i':
+        pool.map(mafftginsi, list_of_files)
+
+    elif strategy == 'Q-INS-i':
+        pool.map(mafftqinsi, list_of_files)
+    
+    result = [file for file in os.listdir(directory) if file.lower().endswith(aligned_extension)]
+    if isTabular(inputFile):
+	with open(directory + os.sep + results, "a") as f:
+	    for file in result:
+	        with open(directory + os.sep + file, "r") as r:
+	            f.write(toData(r.read()) + "\n")
+    else:
+	with open(directory + os.sep + results, "a") as f:
+	    for file in result:
+	        with open(directory + os.sep + file, "r") as r:
+	            f.write(toDataSingle(r.read()) + "\n")
+
+if __name__ == '__main__':
+    main()
+