Mercurial > repos > peterjc > mira4_assembler

annotate tools/mira4/mira4_validator.py @ 20:aeb3e35f8236 draft

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Uploaded v0.0.4 preview, made MAF and BAM output optional
author peterjc
date Tue, 10 Jun 2014 10:11:58 -0400
parents 626d5cfd01aa
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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6
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
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1 #Called from the Galaxy Tool XML file
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2 #import sys
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3
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4 def validate_input(trans, error_map, param_values, page_param_map):
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5 """Validates the min_size/max_size user input, before execution."""
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6 err_list = []
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7 for read_group in param_values["read_group"]:
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8 err = dict()
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9 segments = read_group["segments"]
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10 if str(segments["type"]) != "paired":
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11 err_list.append(dict())
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12 continue
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13
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14 min_size = str(segments["min_size"]).strip()
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15 max_size = str(segments["max_size"]).strip()
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16 #sys.stderr.write("DEBUG min_size=%r, max_size=%r\n" % (min_size, max_size))
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17
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18 #Somehow Galaxy seems to turn an empty field into string "None"...
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19 if min_size=="None":
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20 min_size = ""
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21 if max_size=="None":
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22 max_size = ""
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23
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24 if min_size=="" and max_size=="":
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25 #Both missing is good
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26 pass
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27 elif min_size=="":
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28 err["min_size"] = "Minimum size required if maximum size given"
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29 elif max_size=="":
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30 err["max_size"] = "Maximum size required if minimum size given"
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31
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32 if min_size:
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33 try:
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34 min_size_int = int(min_size)
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35 if min_size_int < 0:
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36 err["min_size"] = "Minumum size must not be negative (%i)" % min_size_int
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37 min_size = None # Avoid doing comparison below
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38 except ValueError:
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39 err["min_size"] = "Minimum size is not an integer (%s)" % min_size
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40 min_size = None # Avoid doing comparison below
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41
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42 if max_size:
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43 try:
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44 max_size_int = int(max_size)
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45 if max_size_int< 0:
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46 err["max_size"] = "Maximum size must not be negative (%i)" % max_size_int
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47 max_size = None # Avoid doing comparison below
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48 except ValueError:
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49 err["max_size"] = "Maximum size is not an integer (%s)" % max_size
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50 max_size = None # Avoid doing comparison below
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51
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52 if min_size and max_size and min_size_int > max_size_int:
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53 msg = "Minimum size must be less than maximum size (%i vs %i)" % (min_size_int, max_size_int)
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54 err["min_size"] = msg
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55 err["max_size"] = msg
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56
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57 if err:
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58 err_list.append({"segments":err})
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59 else:
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60 err_list.append(dict())
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61
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62 if any(err_list):
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63 #Return an error map only if any readgroup gave errors
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64 error_map["read_group"] = err_list