--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phylogenies/phytab_clearcut.py	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,143 @@
+import os
+import optparse
+import subprocess
+from multiprocessing import Pool
+
+directory = ""
+results = "results.data"
+extension = ".fs"
+aligned_extension = ".tre"
+datatype = ""
+
+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, name):
+    name = name.replace("fasta", "") #file name has fasta when fasta file called
+    text = name.replace(".fs.tre", "") + "\t" + text.replace(" " , "")
+    return text
+
+#
+#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 clearcut(input):
+    file_name = directory + os.sep + input
+    popen = subprocess.Popen(['clearcut', "--in=" + file_name, "--out="+file_name + aligned_extension, "--alignment","-k", indata])
+    popen.wait()
+
+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(
+        '-t', '--type',
+        dest='datatype',
+        action='store',
+        type='string',
+        help='-P for protein. -D for DNA.')
+
+    options, args = parser.parse_args()
+
+    global directory
+    global indata
+    inputFile = unescape(options.input)
+    directory = unescape(options.path) + os.sep + "data"
+    indata = "-" + unescape(options.datatype)
+
+    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)]
+    pool.map(clearcut, list_of_files)
+
+    result = [file for file in os.listdir(directory) if file.lower().endswith(aligned_extension)]
+    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(),file))
+
+if __name__ == '__main__':
+    main()