Mercurial > repos > immport-devteam > flowcl

comparison getOntology.py @ 1:f70f75e89890 draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowcl commit d59d95d2bc6a64eb5c37b8291a7c314754c2067f"
author azomics
date Thu, 23 Jul 2020 08:50:18 -0400
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0:fb0ee82f686d 1:f70f75e89890
1 #!/usr/bin/env python
2 ######################################################################
3 # Copyright (c) 2016 Northrop Grumman.
4 # All rights reserved.
5 ######################################################################
6 from __future__ import print_function
7 import sys
8 import os
9
10 from collections import defaultdict
11 from argparse import ArgumentParser
12 from jinja2 import Environment, FileSystemLoader
13
14
15 def generate_flowCL_query(list_markers, list_types):
16 if (len(list_markers) != len(list_types)):
17 return("pb with headers")
18 query = []
19 # go through both lists, remove fsc/ssc
20 for i in range(0, len(list_markers)):
21 if not list_markers[i].startswith("FSC") and not list_markers[i].startswith("SSC"):
22 query.append(list_markers[i].upper())
23 query.append(list_types[i])
24 # return concatenated string
25 return("".join(query))
26
27
28 def run_flowCL(phenotype, output_file, output_dir, tool_dir):
29 os.mkdir(output_dir)
30 tool = "/".join([tool_dir, "getOntology.R"])
31 output_txt = "".join([output_dir, "/flowCL_run_summary.txt"])
32 output_table = "".join([output_dir, "/flowCL_table.txt"])
33 output_pdf = "".join([output_dir, "/flowCL_res.pdf"])
34 run_command = " ". join(["Rscript --slave --vanilla", tool, output_txt, phenotype])
35 os.system(run_command)
36
37 table = defaultdict(list)
38 labels = []
39 nb_match = 0
40 if os.path.isfile(output_txt):
41 with open(output_txt, "r") as txt:
42 check = txt.readline().strip()
43 if (not check):
44 sys.exit(2)
45 else:
46 i = -1
47 for lines in txt:
48 data = lines.strip("\n").split("\"")
49 if data[0].strip():
50 labels.append(data[0].strip())
51 i += 1
52 if data[0].startswith("Score"):
53 count_matches = data[1].split(") ")
54 nb_match = len(count_matches) - 1
55 table[i].append(data[1])
56 else:
57 sys.stderr.write("There are no results with this query. Please check your markers if you believe there should be.")
58 sys.exit(2)
59
60 with open(output_table, "w") as tbl:
61 tbl.write("1\t2\nQuery\t" + phenotype + "\n")
62 for j in table:
63 newline = " ".join(table[j])
64 for k in range(1, nb_match + 1):
65 cur_stg = "".join([str(k+1), ")"])
66 new_stg = "".join(["<br>", cur_stg])
67 newline = newline.replace(cur_stg, new_stg)
68
69 if labels[j] == "Cell ID":
70 cls = newline.split(" ")
71 for m in range(0, len(cls)):
72 if cls[m].startswith("CL"):
73 cl_id = cls[m].replace("_", ":")
74 link = "".join(['<a href="http://www.immport-labs.org/immport-ontology/public/home/home/', cl_id, '" target="_blank">'])
75 cls[m] = "".join([link, cls[m], "</a>"])
76 newline = " ".join(cls)
77 tbl.write("\t".join([labels[j], newline]) + "\n")
78
79 get_graph = " ".join(["mv flowCL_results/*.pdf", output_pdf])
80 os.system(get_graph)
81
82 env = Environment(loader=FileSystemLoader(tool_dir + "/templates"))
83 template = env.get_template("flowCL.template")
84
85 real_directory = output_dir.replace("/job_working_directory", "")
86 context = {'outputDirectory': real_directory}
87 overview = template.render(**context)
88 with open(output_file, "w") as outf:
89 outf.write(overview)
90 return
91
92
93 if __name__ == "__main__":
94 parser = ArgumentParser(
95 prog="getOntology",
96 description="runs flowCL on a set of markers.")
97
98 parser.add_argument(
99 '-m',
100 dest="markers",
101 required=True,
102 action='append',
103 help="marker queries.")
104
105 parser.add_argument(
106 '-y',
107 dest="marker_types",
108 required=True,
109 action='append',
110 help="marker queries.")
111
112 parser.add_argument(
113 '-o',
114 dest="output_file",
115 required=True,
116 help="Name of the output html file.")
117
118 parser.add_argument(
119 '-d',
120 dest="output_dir",
121 required=True,
122 help="Path to the html supporting directory")
123
124 parser.add_argument(
125 '-t',
126 dest="tool_dir",
127 required=True,
128 help="Path to the tool directory")
129
130 args = parser.parse_args()
131
132 markers = [m.strip() for m in args.markers]
133 query = generate_flowCL_query(markers, args.marker_types)
134 run_flowCL(query, args.output_file, args.output_dir, args.tool_dir)