--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/profileCLs.py	Thu Jul 23 08:58:29 2020 -0400
@@ -0,0 +1,161 @@
+#!/usr/bin/env python
+
+######################################################################
+#                  Copyright (c) 2016 Northrop Grumman.
+#                          All rights reserved.
+######################################################################
+import sys
+import os
+from argparse import ArgumentParser
+from jinja2 import Environment, FileSystemLoader
+
+profile_key = {
+    "1": "-",
+    "2": "lo",
+    "3": "+",
+    "4": "hi"
+}
+
+
+def run_flowCL(phenotype, output_txt, output_pdf, tool):
+    run_command = " ". join(["Rscript --slave --vanilla", tool, output_txt, phenotype])
+    os.system(run_command)
+    get_graph = " ".join(["mv flowCL_results/*.pdf", output_pdf])
+    os.system(get_graph)
+    return
+
+
+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(1, 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(profile_key[list_types[i]])
+    # return concatenated string
+    return("".join(query))
+
+
+def translate_profiles(input_file, tool_dir, output, html_dir):
+    os.mkdir(html_dir)
+
+    tool = "/".join([tool_dir, "getOntology.R"])
+    html_table = "".join([html_dir, "/CLprofiles.txt"])
+    score_table = "".join(["cp ", input_file, " ", html_dir, "/scores.txt"])
+    os.system(score_table)
+
+    # read profile
+    with open(input_file, "r") as flock_profiles, open(html_table, "w") as out:
+        headers = flock_profiles.readline()
+        headers = headers.strip()
+        # get all headers except for last 2 (count + percentage)
+        markers = headers.split("\t")[:-2]
+        counter = 0
+
+        out.write("Population\tFlowCL Query\tNb Results\tLink to PDF\t")
+        out.write("Top Result Label\tTop Result Score\tTop Result CL\n")
+        queries = {}
+        # create marker query for each population
+        for lines in flock_profiles:
+            lines = lines.strip("\n")
+            pop_profile = lines.split("\t")[:-2]
+            flowcl_query = generate_flowCL_query(markers, pop_profile)
+            counter += 1
+            nb_results = "0"
+            top_label = "no_match"
+            top_score = "NA"
+            top_CL = "NA"
+            pdf_link = "NA"
+            # check if query was run before
+            if flowcl_query not in queries:
+                # create filenames for results & graphs
+                txt = "".join(["flowcl_pop", str(counter).zfill(2), ".txt"])
+                text_result = "/".join([html_dir, txt])
+                graph = "".join(["flowcl_pop", str(counter).zfill(2), ".pdf"])
+                graph_output = "/".join([html_dir, graph])
+                # run flowCL for each marker profile
+                run_flowCL(flowcl_query, text_result, graph_output, tool)
+
+                # test that text file exists if not results are all NAs:
+                if os.path.isfile(text_result):
+                    with open(text_result, "r") as res:
+                        for line in res:
+                            if line.startswith("Score"):
+                                data = line.split(") ")
+                                top_score = data[2][:-2]
+                                tot_results = len(data) - 2
+                                nb_results = str(tot_results)
+                                if tot_results == 5:
+                                    if len(data[6].split("+")) > 1:
+                                        nb_results = "5+"
+                            elif line.startswith("Cell ID"):
+                                prep_link = line.split(") ")[1][:-2]
+                                cl = prep_link.replace("_", ":")
+                                link = "".join(['<a href="http://www.immport-labs.org/immport-ontology/public/home/home/', cl, '" target="_blank">'])
+                                top_CL = "".join([link, prep_link, "</a>"])
+                            elif line.startswith("Cell Label"):
+                                top_label = line.split(") ")[1][:-2]
+                                pdf_link = "".join(['<a href="', graph, '" target="_blank">PDF</a>'])
+                                tmpflowcl_query = "".join(['<a href="', txt, '" target="_blank">', flowcl_query, '</a>'])
+
+                    queries[flowcl_query] = {
+                        "query": tmpflowcl_query,
+                        "results": nb_results,
+                        "pdf": pdf_link,
+                        "label": top_label,
+                        "score": top_score,
+                        "CL": top_CL
+                    }
+            # write query results to CLprofiles.txt
+            out.write("\t".join([pop_profile[0],
+                                 queries[flowcl_query]["query"],
+                                 queries[flowcl_query]["results"],
+                                 queries[flowcl_query]["pdf"],
+                                 queries[flowcl_query]["label"],
+                                 queries[flowcl_query]["score"],
+                                 queries[flowcl_query]["CL"]]) + "\n")
+
+    env = Environment(loader=FileSystemLoader(tool_dir + "/templates"))
+    template = env.get_template("profileCLs.template")
+
+    real_directory = html_dir.replace("/job_working_directory", "")
+    context = {'outputDirectory': real_directory}
+    overview = template.render(**context)
+    with open(output, "w") as outf:
+        outf.write(overview)
+
+
+if __name__ == "__main__":
+    parser = ArgumentParser(
+             prog="getCLs_from_profile",
+             description="runs flowCL on a each population defined by FLOCK.")
+
+    parser.add_argument(
+            '-i',
+            dest="input_file",
+            required=True,
+            help="File location for the profile.txt from FLOCK.")
+
+    parser.add_argument(
+            '-o',
+            dest="output",
+            required=True,
+            help="Name of the output html file.")
+
+    parser.add_argument(
+            '-d',
+            dest="html_dir",
+            required=True,
+            help="Path to html supporting directory.")
+
+    parser.add_argument(
+            '-t',
+            dest="tool_dir",
+            required=True,
+            help="Path to the tool directory")
+
+    args = parser.parse_args()
+
+    translate_profiles(args.input_file, args.tool_dir, args.output, args.html_dir)