--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/orthologs/hmmsearch.py	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,116 @@
+import os
+import optparse
+import subprocess
+from multiprocessing import Pool
+
+results_dir = "./data"
+results = "results.data"
+result_extension = ".out"
+model_extension = ".hmm"
+database = ""
+
+
+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 unpackData(models):
+    with open(models) as f:
+        for line in f:
+            hmm = HMM(line)
+            with open(results_dir + os.sep + hmm.name + model_extension, "a") as p:
+                # print(hmm.model)
+                p.write(hmm.model)
+
+
+class HMM:
+    def __init__(self, string):
+        lis = string.split('\t')
+        # print lis
+        self.model = self.restoreNewLines(lis[1])
+        self.name = lis[0]
+
+    def restoreNewLines(self, string):
+        return string.replace('\\n', '\n')
+
+
+def toData(text):
+    # lis = text.split()
+    # name = lis[index_of_name_in_hmm]
+    # text = name + "\t" + text.replace("\n", "\\n")
+    # text = text.replace("\n", "\\n")
+    return text
+
+
+def hmmsearch(input):
+    file_name = results_dir + 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(['hmmsearch', "-o", file_name + result_extension, file_name, database])
+    pop.wait()
+
+
+def main():
+    usage = """%prog [options]
+options (listed below) default to 'None' if omitted
+    """
+    parser = optparse.OptionParser(usage=usage)
+
+    parser.add_option(
+        '-i', '--hmm',
+        dest='hmm',
+        action='store',
+        type='string',
+        metavar="FILE",
+        help='Name of input hmm models.')
+
+    parser.add_option(
+        '-d', '--database',
+        dest='database',
+        action='store',
+        type='string',
+        metavar="FILE",
+        help='Name of sequence database.')
+
+    options, args = parser.parse_args()
+
+    global database
+    models = unescape(options.hmm)
+    database = unescape(options.database)
+
+    os.mkdir(results_dir)
+
+    unpackData(models)
+
+    list_of_files = [file for file in os.listdir(results_dir) if file.lower().endswith(model_extension)]
+
+    pool = Pool()
+    pool.map(hmmsearch, list_of_files)
+
+    result = [file for file in os.listdir(results_dir) if file.lower().endswith(result_extension)]
+    with open(results_dir + os.sep + results, "a") as f:
+        for file in result:
+            with open(results_dir + os.sep + file, "r") as r:
+                f.write(toData(r.read()) + "\n")
+
+if __name__ == '__main__':
+    main()