--- a/imgt_locus_split.py	Thu Jul 13 10:24:39 2017 -0400
+++ b/imgt_locus_split.py	Mon Jul 17 08:54:02 2017 -0400
@@ -44,8 +44,8 @@
             shutil.rmtree(check)
 
 
-def filter_tabular_file(old_file, new_file, column, regex):
-    logging.debug("Filtering {0} with {1}".format(old_file, regex.pattern))
+def filter_imgt_file(old_file, new_file, column, fltr):
+    logging.debug("Filtering {0} with {1}".format(old_file, fltr))
     first = True
     total = 0
     remain = 0
@@ -59,7 +59,7 @@
                 nf.write(line)
                 continue
             total += 1
-            if len(splt) >= column_index and regex.search(splt[column_index]):
+            if len(splt) > column_index and splt[column_index].find(fltr) != -1:
                 remain += 1
                 nf.write(line)
     return total, remain
@@ -69,22 +69,21 @@
     return all(l[0] == x for x in l[1:])
 
 
-def filter_imgt_dir(imgt_dir, loci):
-    logging.info("Filtering {0} with {1}".format(imgt_dir, loci))
+def filter_imgt_dir(imgt_dir, locus):
+    logging.info("Working on {0}".format(locus))
     imgt_files = [f for f in os.listdir(imgt_dir) if imgt_file_regex.match(f)]
     tmp_file = os.path.join(imgt_dir, "tmp.txt")
     totals = []
     remains = []
-    loci_regex = re.compile("|".join(loci))
     for imgt_file in imgt_files:
         imgt_file = os.path.join(imgt_dir, imgt_file)
-        total, remain = filter_tabular_file(imgt_file, tmp_file, "V-GENE and allele", loci_regex)
+        total, remain = filter_imgt_file(imgt_file, tmp_file, "V-GENE and allele", locus)
         totals.append(total)
         remains.append(remain)
         logging.debug("{0} rows, {1} after filtering".format(total, remain))
         shutil.move(tmp_file, imgt_file)
     if not (all_same_in_list(totals) and all_same_in_list(remains)):
-        logging.warning("Not all files had the same number of sequences remaining for {0}: {1}".format(imgt_dir, remains))
+        logging.warning("Not all files had the same number of sequences remaining for {0}".format(imgt_dir))
     return totals[0], remains[0]
 
 
@@ -100,9 +99,16 @@
 
 def main():
     parser = argparse.ArgumentParser()
-    parser.add_argument("-i", "--input", help="The input IMGT file", required=True)
-    parser.add_argument("-l", "--loci", help="The Loci to filter on", required=True)
-    parser.add_argument("-o", "--output", help="The output file for the new IMGT zip with just the filtered sequences", required=True)
+    parser.add_argument("--input", help="The input IMGT file", required=True)
+    parser.add_argument("--output-ig", help="The output file for new IMGT ZIP with just IG sequences", default="None")
+    parser.add_argument("--output-igh", help="The output file for new IMGT ZIP with just IGH sequences", default="None")
+    parser.add_argument("--output-igk", help="The output file for new IMGT ZIP with just IGK sequences", default="None")
+    parser.add_argument("--output-igl", help="The output file for new IMGT ZIP with just IGL sequences", default="None")
+    parser.add_argument("--output-tr", help="The output file for new IMGT ZIP with just TR sequences", default="None")
+    parser.add_argument("--output-tra", help="The output file for new IMGT ZIP with just TRA sequences", default="None")
+    parser.add_argument("--output-trb", help="The output file for new IMGT ZIP with just TRB sequences", default="None")
+    parser.add_argument("--output-trd", help="The output file for new IMGT ZIP with just TRD sequences", default="None")
+    parser.add_argument("--output-trg", help="The output file for new IMGT ZIP with just TRG sequences", default="None")
 
     logging.basicConfig(filename="./log.html", level=logging.DEBUG, format="%(asctime)s:&emsp;%(message)s <br />",
                         datefmt='%Y/%m/%d %H:%M:%S')
@@ -111,27 +117,57 @@
 
     args = parser.parse_args()
     input_file = args.input
-    loci = args.loci.split(",")
-    output_file = args.output
+    output_ig = args.output_ig
+    output_igh = args.output_igh
+    output_igk = args.output_igk
+    output_igl = args.output_igl
+    output_tr = args.output_tr
+    output_tra = args.output_tra
+    output_trb = args.output_trb
+    output_trd = args.output_trd
+    output_trg = args.output_trg
+
+    loci = {
+        "IG": output_ig,
+        "IGH": output_igh,
+        "IGK": output_igk,
+        "IGL": output_igl,
+        "TR": output_tr,
+        "TRA": output_tra,
+        "TRB": output_trb,
+        "TRD": output_trd,
+        "TRG": output_trg
+    }
+
+    loci_to_filter = {}
 
     logging.debug("All Parameters:")
     logging.debug("Input: {0}".format(input_file))
-    logging.debug("Loci: {0}".format(loci))
-    logging.debug("Output: {0}".format(output_file))
+    for locus, path in loci.items():
+        logging.debug("{0}: {1}".format(locus, path))
+        if path != "None" and os.path.isdir(os.path.split(path)[0]):
+            loci_to_filter[locus] = path
 
-    if len(loci) == 0:
+    if len(loci_to_filter) == 0:
         raise Exception("No locus selected, nothing to do")
 
+    logging.info("Parameters:")
+    for locus, path in loci_to_filter.items():
+        logging.info("{0}: {1}".format(locus, path))
+
     work_dir = tempfile.mkdtemp()
     original_files_dir = os.path.join(work_dir, "original")
     os.mkdir(original_files_dir)
 
     unpack_imgt_zip(input_file, original_files_dir)
 
-    total, remain = filter_imgt_dir(original_files_dir, loci)
-    logging.info("{0}\t{1}".format(total, remain))
+    for locus, path in loci_to_filter.items():
+        locus_dir = os.path.join(work_dir, locus)
+        shutil.copytree(original_files_dir, locus_dir)
+        total, remain = filter_imgt_dir(locus_dir, locus)
+        logging.info("{0}\t{1}\t{2}\t{3}".format(locus, path, total, remain))
 
-    make_new_xz_file(original_files_dir, output_file)
+        make_new_xz_file(locus_dir, loci_to_filter[locus])
 
 
 if __name__ == "__main__":