Mercurial > repos > george-weingart > maaslin

annotate maaslin-4450aa4ecc84/maaslin_format_input_selector.py @ 1:a87d5a5f2776

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Uploaded the version running on the prod server
author george-weingart
date Sun, 08 Feb 2015 23:08:38 -0500
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1 #!/usr/bin/env python
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2
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3 """
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4 Author: George Weingart
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5 Description: Dynamically read columns from input file for UI
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6 """
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7
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8 #####################################################################################
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9 #Copyright (C) <2012>
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10 #
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11 #Permission is hereby granted, free of charge, to any person obtaining a copy of
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12 #this software and associated documentation files (the "Software"), to deal in the
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13 #Software without restriction, including without limitation the rights to use, copy,
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14 #modify, merge, publish, distribute, sublicense, and/or sell copies of the Software,
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15 #and to permit persons to whom the Software is furnished to do so, subject to
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16 #the following conditions:
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17 #
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18 #The above copyright notice and this permission notice shall be included in all copies
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19 #or substantial portions of the Software.
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20 #
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21 #THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
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22 #INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
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23 #PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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24 #HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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25 #OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
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26 #SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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27 #####################################################################################
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28
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29 __author__ = "George Weingart"
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30 __copyright__ = "Copyright 2012"
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31 __credits__ = ["George Weingart"]
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32 __license__ = "MIT"
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33 __maintainer__ = "George Weingart"
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34 __email__ = "george.weingart@gmail.com"
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35 __status__ = "Development"
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36
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37 import sys,string,time
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38 from pprint import pprint
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39
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40 def red(st,l):
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41 if len(st) <= l: return st
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42 l1,l2 = l/2,l/2
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43 return st[:l1]+".."+st[len(st)-l2:]
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44
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45 def get_cols(data,full_names):
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46 if data == "": return []
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47 max_len =32
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48 fname = data.dataset.file_name
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49 input_file = open(fname)
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50 input_lines = input_file.readlines()
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51 input_file.close()
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52 table_lines = []
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53 for x in input_lines:
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54 first_column = x.split('\t')[0]
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55 table_lines.append(first_column)
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56
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57 opt = []
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58 rc = ''
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59 lines = []
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60 try:
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61 lines = [(red((rc+v.split()[0]),max_len),'%d' % (i+1),False) for i,v in enumerate(table_lines) if v]
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62
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63 except:
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64 l1 = '*ALL*'
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65 l2 = 1
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66 l3 = False
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67 MyList = [l1,l2,l3]
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68 lines.append(MyList)
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69 return opt+lines
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70
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71 def get_cols_add_line(data,full_names,lastmeta):
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72 if data == "": return []
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73 display_to = 1
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74 try:
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75 display_to = int(lastmeta)
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76 except:
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77 pass
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78
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79 max_len = 32
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80 fname = data.dataset.file_name
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81 input_file = open(fname)
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82 input_lines = input_file.readlines()
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83 input_file.close()
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84 table_lines = []
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85 for x in input_lines:
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86 first_column = x.split('\t')[0]
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87 table_lines.append(first_column)
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88 table_lines.insert(0,'-')
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89 if not display_to == 1:
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90 del table_lines[display_to + 1:]
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91
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92
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93 opt = []
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94 rc = ''
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95 lines = []
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96 try:
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97 lines = [(red((rc+v.split()[0]),max_len),'%d' % (i+1),False) for i,v in enumerate(table_lines) if v]
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98
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99 except:
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100 l1 = '*ALL*'
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101 l2 = 1
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102 l3 = False
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103 MyList = [l1,l2,l3]
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104 lines.append(MyList)
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105 return opt+lines
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106
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107 def get_cols_features(data,full_names,lastmeta):
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108 if data == "": return []
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109 display_from = 1
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110 try:
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111 display_from = int(lastmeta)
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112 except:
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113 pass
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114 max_len = 32
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115 fname = data.dataset.file_name
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116 input_file = open(fname)
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117 input_lines = input_file.readlines()
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118 input_file.close()
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119 table_lines = []
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120 for x in input_lines:
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121 first_column = x.split('\t')[0]
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122 table_lines.append(first_column)
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123
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124 opt = []
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125 rc = ''
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126 del table_lines[:display_from]
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127 lines = []
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128 try:
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129 lines = [(red((rc+v.split()[0]),max_len),'%d' % (i+1),False) for i,v in enumerate(table_lines) if v]
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130
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131 except:
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132 l1 = '*ALL*'
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133 l2 = 1
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134 l3 = False
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135 MyList = [l1,l2,l3]
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136 lines.append(MyList)
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137 return opt+lines