--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/orthologs/hmmbuild.py	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,106 @@
+import os
+import optparse
+import subprocess
+from multiprocessing import Pool
+
+directory = "./data"
+results = "results.data"
+extension = ".afa"
+model_extension = ".hmm"
+inputFile = ""
+index_of_name_in_hmm = 6
+
+
+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 toData(text):
+    lis = text.split()
+    name = lis[index_of_name_in_hmm]
+    text = name + "\t" + text.replace("\n", "\\n")
+    return text
+
+
+def hmmbuild(input):
+    file_name = directory + os.sep + input
+    # print file_name
+    # return subprocess.Popen(['hmmbuild', "--informat", "afa", file_name + ".hmm", file_name], stdout=subprocess.PIPE).communicate()[0]  # ./muscle
+    pop = subprocess.Popen(['hmmbuild', "--informat", "afa", file_name + ".hmm", file_name])
+    pop.wait()
+
+
+class Sequence:
+    def __init__(self, string):
+        lis = string.split('\t')
+        # print lis
+        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 main():
+    usage = """%prog [options]
+options (listed below) default to 'None' if omitted
+    """
+    parser = optparse.OptionParser(usage=usage)
+
+    parser.add_option(
+        '-i', '--in',
+        dest='input',
+        action='store',
+        type='string',
+        metavar="FILE",
+        help='Name of input data.')
+
+    options, args = parser.parse_args()
+
+    global inputFile, directory
+    inputFile = unescape(options.input)
+
+    os.mkdir(directory)
+
+    with open(inputFile) as f:
+        for line in f:
+            seq = Sequence(line)
+            with open(directory + os.sep + seq.family + extension, "a") as p:
+                p.write(seq.printFASTA())
+
+    pool = Pool()
+    list_of_files = [file for file in os.listdir(directory) if file.lower().endswith(extension)]
+
+    pool.map(hmmbuild, list_of_files)
+
+    result = [file for file in os.listdir(directory) if file.lower().endswith(model_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()) + "\n")
+
+if __name__ == '__main__':
+    main()