Mercurial > repos > peterjc > mira4_assembler

comparison tools/mira4/mira4_validator.py @ 6:626d5cfd01aa draft

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Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
author peterjc
date Mon, 21 Oct 2013 12:01:47 -0400
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5:ffefb87bd414 6:626d5cfd01aa
1 #Called from the Galaxy Tool XML file
2 #import sys
3
4 def validate_input(trans, error_map, param_values, page_param_map):
5 """Validates the min_size/max_size user input, before execution."""
6 err_list = []
7 for read_group in param_values["read_group"]:
8 err = dict()
9 segments = read_group["segments"]
10 if str(segments["type"]) != "paired":
11 err_list.append(dict())
12 continue
13
14 min_size = str(segments["min_size"]).strip()
15 max_size = str(segments["max_size"]).strip()
16 #sys.stderr.write("DEBUG min_size=%r, max_size=%r\n" % (min_size, max_size))
17
18 #Somehow Galaxy seems to turn an empty field into string "None"...
19 if min_size=="None":
20 min_size = ""
21 if max_size=="None":
22 max_size = ""
23
24 if min_size=="" and max_size=="":
25 #Both missing is good
26 pass
27 elif min_size=="":
28 err["min_size"] = "Minimum size required if maximum size given"
29 elif max_size=="":
30 err["max_size"] = "Maximum size required if minimum size given"
31
32 if min_size:
33 try:
34 min_size_int = int(min_size)
35 if min_size_int < 0:
36 err["min_size"] = "Minumum size must not be negative (%i)" % min_size_int
37 min_size = None # Avoid doing comparison below
38 except ValueError:
39 err["min_size"] = "Minimum size is not an integer (%s)" % min_size
40 min_size = None # Avoid doing comparison below
41
42 if max_size:
43 try:
44 max_size_int = int(max_size)
45 if max_size_int< 0:
46 err["max_size"] = "Maximum size must not be negative (%i)" % max_size_int
47 max_size = None # Avoid doing comparison below
48 except ValueError:
49 err["max_size"] = "Maximum size is not an integer (%s)" % max_size
50 max_size = None # Avoid doing comparison below
51
52 if min_size and max_size and min_size_int > max_size_int:
53 msg = "Minimum size must be less than maximum size (%i vs %i)" % (min_size_int, max_size_int)
54 err["min_size"] = msg
55 err["max_size"] = msg
56
57 if err:
58 err_list.append({"segments":err})
59 else:
60 err_list.append(dict())
61
62 if any(err_list):
63 #Return an error map only if any readgroup gave errors
64 error_map["read_group"] = err_list