# HG changeset patch
# User immport-devteam
# Date 1488218194 18000
# Node ID fb0ee82f686d2e72736169ea1541f17e87056a4b
Uploaded
diff -r 000000000000 -r fb0ee82f686d flowcl/getOntology.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/flowcl/getOntology.R Mon Feb 27 12:56:34 2017 -0500
@@ -0,0 +1,28 @@
+# Cell Ontology Module for Galaxy
+# FlowCL
+######################################################################
+# Copyright (c) 2016 Northrop Grumman.
+# All rights reserved.
+######################################################################
+#
+# Version 1
+# Cristel Thomas
+#
+#
+
+library(flowCL)
+library(base)
+
+getOntology <- function(output_file, markers) {
+ res <- flowCL(markers, ResetArch = TRUE)
+ if (length(res) == 6) {
+ report <- capture.output(res$Table)
+ sink(output_file)
+ cat(report, sep = "\n")
+ sink()
+ }
+}
+
+args <- commandArgs(trailingOnly = TRUE)
+markers <- paste(args[3:length(args)], collapse="")
+getOntology(args[2], markers)
diff -r 000000000000 -r fb0ee82f686d flowcl/getOntology.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/flowcl/getOntology.py Mon Feb 27 12:56:34 2017 -0500
@@ -0,0 +1,135 @@
+#!/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, "--args", 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(["
", 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([''])
+ cls[m] = "".join([link, cls[m], ""])
+ 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)
+ sys.exit(0)
diff -r 000000000000 -r fb0ee82f686d flowcl/getOntology.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/flowcl/getOntology.xml Mon Feb 27 12:56:34 2017 -0500
@@ -0,0 +1,102 @@
+
+ given a phenotype using flowCL.
+
+ jinja2
+ r
+ bioconductor-flowcl
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 10.1093/bioinformatics/btu807
+
+
diff -r 000000000000 -r fb0ee82f686d flowcl/static/flowtools/css/flowCL.css
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/flowcl/static/flowtools/css/flowCL.css Mon Feb 27 12:56:34 2017 -0500
@@ -0,0 +1,43 @@
+/*
+** DataTables config
+*/
+div.dt-buttons {
+ float: right;
+}
+
+th {
+ font-size:16px;
+ text-align: left;
+}
+
+body td {
+ max-width: 50px;
+ font-size: 14px;
+ overflow: hidden;
+ text-overflow: ellipsis;
+}
+
+.cltable thead {
+ display:none;
+}
+
+.cltable td {
+ max-width: 40px;
+ word-break: break-all;
+ word-wrap: break-word;
+}
+
+.firstcol {
+ width: 160px;
+}
+
+.smallcols {
+ width: 100px;
+}
+
+div.dataTables_wrapper {
+ width: 95%;
+ margin: 0 auto;
+}
+
+
diff -r 000000000000 -r fb0ee82f686d flowcl/static/flowtools/js/flowcl_table.js
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/flowcl/static/flowtools/js/flowcl_table.js Mon Feb 27 12:56:34 2017 -0500
@@ -0,0 +1,28 @@
+// Copyright (c) 2016 Northrop Grumman.
+// All rights reserved.
+
+var flowcl_table = './flowCL_table.txt';
+
+var displayFlowCLTable = function(){
+ d3.tsv(flowcl_table, function(error, data){
+ if (error){
+ alert("Problem retrieving data");
+ return;
+ }
+ var fclHTML = '';
+ $('#flowcl').html(fclHTML);
+
+ var fclTableData = $.extend(true, [], data);
+ var fclTable = $('#flowcltable').DataTable({
+ columns: [
+ {"data":"1", className: 'firstcol'},
+ {"data":"2"}
+ ],
+ dom: 't',
+ data: fclTableData,
+ buttons: [
+ 'copy', 'pdfHtml5','csvHtml5'
+ ]
+ });
+ });
+};
diff -r 000000000000 -r fb0ee82f686d flowcl/static/images/flowtools/flowcl_graph.png
Binary file flowcl/static/images/flowtools/flowcl_graph.png has changed
diff -r 000000000000 -r fb0ee82f686d flowcl/static/images/flowtools/flowcl_summary.png
Binary file flowcl/static/images/flowtools/flowcl_summary.png has changed
diff -r 000000000000 -r fb0ee82f686d flowcl/templates/flowCL.template
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/flowcl/templates/flowCL.template Mon Feb 27 12:56:34 2017 -0500
@@ -0,0 +1,80 @@
+
+
+
+Flow CL Results
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r fb0ee82f686d flowcl/test-data/flowCL_res.pdf
Binary file flowcl/test-data/flowCL_res.pdf has changed
diff -r 000000000000 -r fb0ee82f686d flowcl/test-data/flowCL_run_summary.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/flowcl/test-data/flowCL_run_summary.txt Mon Feb 27 12:56:34 2017 -0500
@@ -0,0 +1,24 @@
+ [,1]
+Short marker names "CD4+"
+Ontology marker names "CD4 molecule"
+Experiment markers "CD4"
+Ontology exper. names "CD4 molecule"
+Successful Match? "No"
+Marker ID "1) PR_000001004 2) PR_000001004 3) PR_000001004 4) PR_000001004 5)"
+ "PR_000001004 + more"
+Marker Label "1) CD4 molecule 2) CD4 molecule 3) CD4 molecule 4) CD4 molecule 5)"
+ "CD4 molecule + more"
+Marker Key "1) { } CD4+ ( ) [ alpha-beta T cell receptor complex+, T cell"
+ "receptor co-receptor CD8+ ] 2) { } CD4+ ( ) [ alpha-beta T cell"
+ "receptor complex+, T cell receptor co-receptor CD8+ ] 3) { } CD4+ ( )"
+ "[ alpha-beta T cell receptor complex+, T cell receptor co-receptor"
+ "CD8+ ] 4) { } CD4+ ( ) [ T-cell surface glycoprotein CD8 alpha"
+ "chain-, alpha-beta T cell receptor complex+ ] 5) { } CD4+ ( ) [ T"
+ "cell receptor co-receptor CD8-, alpha-beta T cell receptor complex+,"
+ "CD3+ ] + more"
+Score (Out of 1) "1) 0.333 2) 0.333 3) 0.333 4) 0.333 5) 0.25 + more"
+Cell ID "1) CL_0000809 2) CL_0002427 3) CL_0002428 4) CL_0000810 5) CL_0000492"
+ "+ more"
+Cell Label "1) double-positive, alpha-beta thymocyte 2) resting double-positive"
+ "thymocyte 3) double-positive blast 4) CD4-positive, alpha-beta"
+ "thymocyte 5) CD4-positive helper T cell + more"
diff -r 000000000000 -r fb0ee82f686d flowcl/test-data/flowCL_table.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/flowcl/test-data/flowCL_table.txt Mon Feb 27 12:56:34 2017 -0500
@@ -0,0 +1,12 @@
+1 2
+Short marker names CD4+
+Ontology marker names CD4 molecule
+Experiment markers CD4
+Ontology exper. names CD4 molecule
+Successful Match? No
+Marker ID 1) PR_000001004
2) PR_000001004
3) PR_000001004
4) PR_000001004
5) PR_000001004 + more
+Marker Label 1) CD4 molecule
2) CD4 molecule
3) CD4 molecule
4) CD4 molecule
5) CD4 molecule + more
+Marker Key 1) { } CD4+ ( ) [ alpha-beta T cell receptor complex+, T cell receptor co-receptor CD8+ ]
2) { } CD4+ ( ) [ alpha-beta T cell receptor complex+, T cell receptor co-receptor CD8+ ]
3) { } CD4+ ( ) [ alpha-beta T cell receptor complex+, T cell receptor co-receptor CD8+ ]
4) { } CD4+ ( ) [ T-cell surface glycoprotein CD8 alpha chain-, alpha-beta T cell receptor complex+ ]
5) { } CD4+ ( ) [ T cell receptor co-receptor CD8-, alpha-beta T cell receptor complex+, CD3+ ] + more
+Score (Out of 1) 1) 0.333
2) 0.333
3) 0.333
4) 0.333
5) 0.25 + more
+Cell ID 1) CL_0000809
2) CL_0002427
3) CL_0002428
4) CL_0000810
5) CL_0000492 + more
+Cell Label 1) double-positive, alpha-beta thymocyte
2) resting double-positive thymocyte
3) double-positive blast
4) CD4-positive, alpha-beta thymocyte
5) CD4-positive helper T cell + more
diff -r 000000000000 -r fb0ee82f686d flowcl/test-data/out.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/flowcl/test-data/out.html Mon Feb 27 12:56:34 2017 -0500
@@ -0,0 +1,80 @@
+
+
+
+Flow CL Results
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file