--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getOntology.py	Thu Jul 23 08:50:18 2020 -0400
@@ -0,0 +1,134 @@
+#!/usr/bin/env python
+######################################################################
+#                  Copyright (c) 2016 Northrop Grumman.
+#                          All rights reserved.
+######################################################################
+from __future__ import print_function
+import sys
+import os
+
+from collections import defaultdict
+from argparse import ArgumentParser
+from jinja2 import Environment, FileSystemLoader
+
+
+def generate_flowCL_query(list_markers, list_types):
+    if (len(list_markers) != len(list_types)):
+        return("pb with headers")
+    query = []
+    # go through both lists, remove fsc/ssc
+    for i in range(0, len(list_markers)):
+        if not list_markers[i].startswith("FSC") and not list_markers[i].startswith("SSC"):
+            query.append(list_markers[i].upper())
+            query.append(list_types[i])
+    # return concatenated string
+    return("".join(query))
+
+
+def run_flowCL(phenotype, output_file, output_dir, tool_dir):
+    os.mkdir(output_dir)
+    tool = "/".join([tool_dir, "getOntology.R"])
+    output_txt = "".join([output_dir, "/flowCL_run_summary.txt"])
+    output_table = "".join([output_dir, "/flowCL_table.txt"])
+    output_pdf = "".join([output_dir, "/flowCL_res.pdf"])
+    run_command = " ". join(["Rscript --slave --vanilla", tool, output_txt, phenotype])
+    os.system(run_command)
+
+    table = defaultdict(list)
+    labels = []
+    nb_match = 0
+    if os.path.isfile(output_txt):
+        with open(output_txt, "r") as txt:
+            check = txt.readline().strip()
+            if (not check):
+                sys.exit(2)
+            else:
+                i = -1
+                for lines in txt:
+                    data = lines.strip("\n").split("\"")
+                    if data[0].strip():
+                        labels.append(data[0].strip())
+                        i += 1
+                        if data[0].startswith("Score"):
+                            count_matches = data[1].split(") ")
+                            nb_match = len(count_matches) - 1
+                    table[i].append(data[1])
+    else:
+        sys.stderr.write("There are no results with this query. Please check your markers if you believe there should be.")
+        sys.exit(2)
+
+    with open(output_table, "w") as tbl:
+        tbl.write("1\t2\nQuery\t" + phenotype + "\n")
+        for j in table:
+            newline = " ".join(table[j])
+            for k in range(1, nb_match + 1):
+                cur_stg = "".join([str(k+1), ")"])
+                new_stg = "".join(["<br>", cur_stg])
+                newline = newline.replace(cur_stg, new_stg)
+
+            if labels[j] == "Cell ID":
+                cls = newline.split(" ")
+                for m in range(0, len(cls)):
+                    if cls[m].startswith("CL"):
+                        cl_id = cls[m].replace("_", ":")
+                        link = "".join(['<a href="http://www.immport-labs.org/immport-ontology/public/home/home/', cl_id, '" target="_blank">'])
+                        cls[m] = "".join([link, cls[m], "</a>"])
+                newline = " ".join(cls)
+            tbl.write("\t".join([labels[j], newline]) + "\n")
+
+    get_graph = " ".join(["mv flowCL_results/*.pdf", output_pdf])
+    os.system(get_graph)
+
+    env = Environment(loader=FileSystemLoader(tool_dir + "/templates"))
+    template = env.get_template("flowCL.template")
+
+    real_directory = output_dir.replace("/job_working_directory", "")
+    context = {'outputDirectory': real_directory}
+    overview = template.render(**context)
+    with open(output_file, "w") as outf:
+        outf.write(overview)
+    return
+
+
+if __name__ == "__main__":
+    parser = ArgumentParser(
+             prog="getOntology",
+             description="runs flowCL on a set of markers.")
+
+    parser.add_argument(
+            '-m',
+            dest="markers",
+            required=True,
+            action='append',
+            help="marker queries.")
+
+    parser.add_argument(
+            '-y',
+            dest="marker_types",
+            required=True,
+            action='append',
+            help="marker queries.")
+
+    parser.add_argument(
+            '-o',
+            dest="output_file",
+            required=True,
+            help="Name of the output html file.")
+
+    parser.add_argument(
+            '-d',
+            dest="output_dir",
+            required=True,
+            help="Path to the html supporting directory")
+
+    parser.add_argument(
+            '-t',
+            dest="tool_dir",
+            required=True,
+            help="Path to the tool directory")
+
+    args = parser.parse_args()
+
+    markers = [m.strip() for m in args.markers]
+    query = generate_flowCL_query(markers, args.marker_types)
+    run_flowCL(query, args.output_file, args.output_dir, args.tool_dir)