annotate query_tabular.py @ 11:fd16243931d6 draft

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author jjohnson
date Fri, 12 May 2017 10:18:42 -0400
parents e84d1c3bf4fe
children 5b4f6cf857cf
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1 #!/usr/bin/env python
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2 """
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3 """
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4 import sys
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5 import re
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6 import os.path
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7 import json
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8 import sqlite3 as sqlite
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9 import optparse
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10 from optparse import OptionParser
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11
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12 """
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13 TODO:
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14 - could read column names from comment lines, but issues with legal names
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15 - could add some transformations on tabular columns,
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16 filter - skip_regex
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17 e.g. a regex to format date/time strings
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18 format: {
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19 c2 : re.sub('pat', 'sub', c2)
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20 c3 : len(c3)
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21 }
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22 def format(colname,val, expr):
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23 normalize input list columns
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24 iterate over list values creating one row per iteration
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25 option for input line_num column
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26 create associated table
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27 fk, name, value # e.g. PSM table with list of proteins containing peptide
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28 fk, name, value[, value] # if multiple columns similarly indexed, e.g. vcf
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29 - column_defs dict of columns to create from tabular input
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30 column_defs : { 'name1' : 'expr', 'name2' : 'expr'}
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31 - allow multiple queries and outputs
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32 repeat min - max with up to max conditional outputs
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33
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34 - add a --json input for table definitions (or yaml)
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35 JSON config:
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36 { tables : [
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37 { file_path : '/home/galaxy/dataset_101.dat',
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38 table_name : 't1',
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39 column_names : ['c1', 'c2', 'c3'],
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40 pkey_autoincr : 'id'
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41 comment_lines : 1
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42 unique: ['c1'],
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43 index: ['c2','c3']
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44 },
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45 { file_path : '/home/galaxy/dataset_102.dat',
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46 table_name : 'gff',
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47 column_names : ['seqname',,'date','start','end']
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48 comment_lines : 1
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49 load_named_columns : True
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50 filters : [{'filter': 'regex', 'pattern': '#peptide', 'action': 'exclude_match'},
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51 {'filter': 'replace', 'column': 3, 'replace': 'gi[|]', 'pattern': ''}]
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52 },
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53 { file_path : '/home/galaxy/dataset_103.dat',
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54 table_name : 'test',
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55 column_names : ['c1', 'c2', 'c3']
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56 }
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57 ]
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58 }
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59 """
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60
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61
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62 class LineFilter( object ):
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63 def __init__(self,source,filter_dict):
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64 self.source = source
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65 self.filter_dict = filter_dict
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66 # print >> sys.stderr, 'LineFilter %s' % filter_dict if filter_dict else 'NONE'
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67 self.func = lambda i,l: l.rstrip('\r\n') if l else None
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68 self.src_lines = []
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69 self.src_line_cnt = 0
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70 if not filter_dict:
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71 return
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72 if filter_dict['filter'] == 'regex':
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73 rgx = re.compile(filter_dict['pattern'])
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74 if filter_dict['action'] == 'exclude_match':
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75 self.func = lambda i,l: l if not rgx.match(l) else None
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76 elif filter_dict['action'] == 'include_match':
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77 self.func = lambda i,l: l if rgx.match(l) else None
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78 elif filter_dict['action'] == 'exclude_find':
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79 self.func = lambda i,l: l if not rgx.search(l) else None
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80 elif filter_dict['action'] == 'include_find':
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81 self.func = lambda i,l: l if rgx.search(l) else None
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82 elif filter_dict['filter'] == 'replace':
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83 p = filter_dict['pattern']
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84 r = filter_dict['replace']
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85 c = int(filter_dict['column']) - 1
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86 self.func = lambda i,l: '\t'.join([x if i != c else re.sub(p,r,x) for i,x in enumerate(l.split('\t'))])
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87 elif filter_dict['filter'] == 'prepend_line_num':
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88 self.func = lambda i,l: '%d\t%s' % (i,l)
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89 elif filter_dict['filter'] == 'append_line_num':
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90 self.func = lambda i,l: '%s\t%d' % (l.rstrip('\r\n'),i)
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91 elif filter_dict['filter'] == 'skip':
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92 cnt = filter_dict['count']
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93 self.func = lambda i,l: l if i > cnt else None
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94 elif filter_dict['filter'] == 'normalize':
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95 cols = [int(c) - 1 for c in filter_dict['columns']]
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96 sep = filter_dict['separator']
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97 self.func = lambda i,l: self.normalize(l,cols,sep)
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98 def __iter__(self):
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99 return self
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100 def normalize(self,line,split_cols,sep):
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101 lines = []
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102 fields = line.rstrip('\r\n').split('\t')
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103 split_fields = dict()
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104 cnt = 0
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105 for c in split_cols:
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106 if c < len(fields):
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107 split_fields[c] = fields[c].split(sep)
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108 cnt = max(cnt, len(split_fields[c]))
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109 if cnt == 0:
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110 lines.append('\t'.join(fields))
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111 else:
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112 for n in range(0, cnt):
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113 flds = [x if c not in split_cols else split_fields[c][n] if n < len(split_fields[c]) else '' for (c, x) in enumerate(fields)]
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114 lines.append('\t'.join(flds))
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115 return lines
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116 def get_lines(self):
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117 for i,next_line in enumerate(self.source):
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118 self.src_line_cnt += 1
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119 line = self.func(self.src_line_cnt,next_line)
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120 # print >> sys.stderr, 'LineFilter %s: %d %s' % (str(self.filter_dict),self.src_line_cnt,line)
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121 if line:
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122 if isinstance(line,list):
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123 self.src_lines.extend(line)
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124 else:
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125 self.src_lines.append(line)
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126 return
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127 def next(self):
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128 if not self.src_lines:
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129 self.get_lines()
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130 if self.src_lines:
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131 return self.src_lines.pop(0)
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132 raise StopIteration
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133
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134
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135 class TabularReader:
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136 """
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137 Tabular file iterator. Returns a list
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138 """
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139 def __init__(self, file_path, skip=0, comment_char=None, col_idx=None, filters=None):
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140 self.skip = skip
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141 self.comment_char = comment_char
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142 self.col_idx = col_idx
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143 self.filters = filters
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144 self.tsv_file = open(file_path)
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145 if skip and skip > 0:
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146 for i in range(skip):
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147 if not self.tsv_file.readline():
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148 break
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149 source = LineFilter(self.tsv_file,None)
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150 if comment_char:
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151 source = LineFilter(source,{"filter": "regex", "pattern": comment_char, "action": "exclude_match"})
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152 if filters:
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153 for f in filters:
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154 source = LineFilter(source,f)
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155 self.source = source
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156 def __iter__(self):
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157 return self
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158 def next(self):
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159 ''' Iteration '''
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160 for i,line in enumerate(self.source):
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161 fields = line.rstrip('\r\n').split('\t')
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162 if self.col_idx:
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163 fields = [fields[i] for i in self.col_idx]
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164 return fields
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165 raise StopIteration
0
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166
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167
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168 def getValueType(val):
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169 if val or 0. == val:
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170 try:
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171 int(val)
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172 return 'INTEGER'
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173 except:
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174 try:
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175 float(val)
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176 return 'REAL'
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177 except:
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178 return 'TEXT'
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179 return None
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180
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181
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182 def get_column_def(file_path, table_name, skip=0, comment_char='#',
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183 column_names=None, max_lines=100,load_named_columns=False,filters=None):
0
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184 col_pref = ['TEXT', 'REAL', 'INTEGER', None]
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185 col_types = []
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186 col_idx = None
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187 data_lines = 0
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188 try:
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189 tr = TabularReader(file_path,skip=skip, comment_char=comment_char, col_idx=None, filters=filters)
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190 for linenum, fields in enumerate(tr):
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191 if linenum > max_lines:
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192 break
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193 try:
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194 while len(col_types) < len(fields):
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195 col_types.append(None)
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196 for i, val in enumerate(fields):
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197 colType = getValueType(val)
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198 if col_pref.index(colType) < col_pref.index(col_types[i]):
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199 col_types[i] = colType
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200 except Exception, e:
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201 print >> sys.stderr, 'Failed at line: %d err: %s' % (linenum, e)
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202 except Exception, e:
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203 print >> sys.stderr, 'Failed: %s' % (e)
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204 for i,col_type in enumerate(col_types):
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205 if not col_type:
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206 col_types[i] = 'TEXT'
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207 if column_names:
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208 col_names = []
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209 if load_named_columns:
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210 col_idx = []
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211 for i, cname in enumerate([cn.strip() for cn in column_names.split(',')]):
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212 if cname != '':
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213 col_idx.append(i)
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214 col_names.append(cname)
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215 col_types = [col_types[i] for i in col_idx]
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216 else:
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217 col_names = ['c%d' % i for i in range(1, len(col_types) + 1)]
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218 for i, cname in enumerate([cn.strip() for cn in column_names.split(',')]):
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219 if cname and i < len(col_names):
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220 col_names[i] = cname
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221 else:
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222 col_names = ['c%d' % i for i in range(1, len(col_types) + 1)]
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223 col_def = []
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224 for i, col_name in enumerate(col_names):
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225 col_def.append('%s %s' % (col_names[i], col_types[i]))
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226 return col_names, col_types, col_def, col_idx
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227
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228
6
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229 def create_table(conn, file_path, table_name, skip=0, comment_char='#', pkey_autoincr=None, column_names=None,load_named_columns=False,filters=None,unique_indexes=[],indexes=[]):
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230
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231 col_names, col_types, col_def, col_idx = get_column_def(file_path, table_name, skip=skip, comment_char=comment_char,
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232 column_names=column_names,load_named_columns=load_named_columns,filters=filters)
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233 col_func = [float if t == 'REAL' else int if t == 'INTEGER' else str for t in col_types]
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234 table_def = 'CREATE TABLE %s (\n %s%s\n);' % (
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235 table_name,
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236 '%s INTEGER PRIMARY KEY AUTOINCREMENT,' % pkey_autoincr if pkey_autoincr else '',
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237 ', \n '.join(col_def))
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238 # print >> sys.stdout, table_def
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239 insert_stmt = 'INSERT INTO %s(%s) VALUES(%s)' % (table_name, ','.join(col_names), ','.join(["?" for x in col_names]))
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240 # print >> sys.stdout, insert_stmt
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241 data_lines = 0
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242 try:
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243 c = conn.cursor()
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244 c.execute(table_def)
4
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245 conn.commit()
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246 c.close()
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247 for i,index in enumerate(unique_indexes):
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248 index_name='idx_uniq_%s_%d' % (table_name,i)
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249 index_columns = index.split(',')
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250 create_index(conn, table_name, index_name, index_columns,unique=True)
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251 for i,index in enumerate(indexes):
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252 index_name='idx_%s_%d' % (table_name,i)
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253 index_columns = index.split(',')
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254 create_index(conn, table_name, index_name, index_columns)
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255 c = conn.cursor()
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256 tr = TabularReader(file_path,skip=skip, comment_char=comment_char, col_idx=col_idx, filters=filters)
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257 for linenum, fields in enumerate(tr):
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258 data_lines += 1
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259 try:
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260 vals = [col_func[i](x) if x else None for i, x in enumerate(fields)]
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261 c.execute(insert_stmt, vals)
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262 except Exception, e:
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263 print >> sys.stderr, 'Failed at line: %d err: %s' % (linenum, e)
0
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264 conn.commit()
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265 c.close()
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266 except Exception, e:
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267 print >> sys.stderr, 'Failed: %s' % (e)
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268 exit(1)
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269
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270
4
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271 def create_index(conn, table_name, index_name, index_columns, unique=False):
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272 index_def = "CREATE %s INDEX %s on %s(%s)" % ('UNIQUE' if unique else '', index_name, table_name, ','.join(index_columns))
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273 c = conn.cursor()
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274 c.execute(index_def)
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275 conn.commit()
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276 c.close()
0
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277
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278
0
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279 def regex_match(expr, item):
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280 return re.match(expr, item) is not None
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281
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282
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283 def regex_search(expr, item):
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284 return re.search(expr, item) is not None
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285
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286
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287 def regex_sub(expr, replace, item):
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288 return re.sub(expr, replace, item)
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289
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290
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291 def get_connection(sqlitedb_path, addfunctions=False):
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292 conn = sqlite.connect(sqlitedb_path)
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293 if addfunctions:
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294 conn.create_function("re_match", 2, regex_match)
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295 conn.create_function("re_search", 2, regex_search)
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296 conn.create_function("re_sub", 3, regex_sub)
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297 return conn
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298
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299
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300 def __main__():
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301 # Parse Command Line
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302 parser = optparse.OptionParser()
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303 parser.add_option('-s', '--sqlitedb', dest='sqlitedb', default=None, help='The SQLite Database')
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304 parser.add_option('-t', '--table', dest='tables', action="append", default=[], help='Tabular file: file_path[=table_name[:column_name, ...]')
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305 parser.add_option('-j', '--jsonfile', dest='jsonfile', default=None, help='Tabular file: file_path[=table_name[:column_name, ...]')
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306 parser.add_option('-q', '--query', dest='query', default=None, help='SQL query')
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307 parser.add_option('-Q', '--query_file', dest='query_file', default=None, help='SQL query file')
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308 parser.add_option('-n', '--no_header', dest='no_header', action='store_true', default=False, help='Include a column headers line')
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309 parser.add_option('-o', '--output', dest='output', default=None, help='Output file for query results')
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310 (options, args) = parser.parse_args()
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311
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312 # open sqlite connection
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313 conn = get_connection(options.sqlitedb)
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314 # determine output destination
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315 if options.output is not None:
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316 try:
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317 outputPath = os.path.abspath(options.output)
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318 outputFile = open(outputPath, 'w')
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319 except Exception, e:
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320 print >> sys.stderr, "failed: %s" % e
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321 exit(3)
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322 else:
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323 outputFile = sys.stdout
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324
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325 # get table defs
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326 if options.tables:
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327 for ti, table in enumerate(options.tables):
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328 table_name = 't%d' % (ti + 1)
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329 column_names = None
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330 fields = table.split('=')
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331 path = fields[0]
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332 if len(fields) > 1:
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333 names = fields[1].split(':')
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334 table_name = names[0] if names[0] else table_name
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335 if len(names) > 1:
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336 column_names = names[1]
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337 # print >> sys.stdout, '%s %s' % (table_name, path)
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338 create_table(conn, path, table_name, column_names=column_names)
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339 if options.jsonfile:
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340 try:
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341 fh = open(options.jsonfile)
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342 tdef = json.load(fh)
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343 if 'tables' in tdef:
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344 for ti, table in enumerate(tdef['tables']):
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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345 path = table['file_path']
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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346 table_name = table['table_name'] if 'table_name' in table else 't%d' % (ti + 1)
3
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347 comment_lines = table['comment_lines'] if 'comment_lines' in table else 0
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348 comment_char = table['comment_char'] if 'comment_char' in table else None
0
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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349 column_names = table['column_names'] if 'column_names' in table else None
3
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350 if column_names:
3e3b3c883bec planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty
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351 load_named_columns = table['load_named_columns'] if 'load_named_columns' in table else False
3e3b3c883bec planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty
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352 else:
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353 load_named_columns = False
4
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354 unique_indexes = table['unique'] if 'unique' in table else []
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355 indexes = table['index'] if 'index' in table else []
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356 filters = table['filters'] if 'filters' in table else None
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357 pkey_autoincr = table['pkey_autoincr'] if 'pkey_autoincr' in table else None
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358 create_table(conn, path, table_name, pkey_autoincr=pkey_autoincr, column_names=column_names,
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359 skip=comment_lines, comment_char=comment_char, load_named_columns=load_named_columns,
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360 filters=filters,unique_indexes=unique_indexes, indexes=indexes)
0
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361 except Exception, exc:
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362 print >> sys.stderr, "Error: %s" % exc
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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363 conn.close()
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jjohnson
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364
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365 query = None
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jjohnson
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366 if (options.query_file is not None):
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367 with open(options.query_file, 'r') as fh:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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368 query = ''
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jjohnson
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369 for line in fh:
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370 query += line
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jjohnson
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371 elif (options.query is not None):
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372 query = options.query
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373
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374 if (query is None):
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375 tables_query = \
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376 "SELECT name, sql FROM sqlite_master WHERE type='table' ORDER BY name"
0
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377 try:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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378 conn = get_connection(options.sqlitedb)
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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379 c = conn.cursor()
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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380 rslt = c.execute(tables_query).fetchall()
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381 for table, sql in rslt:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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382 print >> sys.stderr, "Table %s:" % table
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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383 try:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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384 col_query = 'SELECT * FROM %s LIMIT 0' % table
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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385 cur = conn.cursor().execute(col_query)
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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386 cols = [col[0] for col in cur.description]
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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387 print >> sys.stderr, " Columns: %s" % cols
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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388 except Exception, exc:
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389 print >> sys.stderr, "Error: %s" % exc
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390 except Exception, exc:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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391 print >> sys.stderr, "Error: %s" % exc
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392 exit(0)
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393 # if not sqlite.is_read_only_query(query):
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394 # print >> sys.stderr, "Error: Must be a read only query"
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395 # exit(2)
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396 try:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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397 conn = get_connection(options.sqlitedb, addfunctions=True)
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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398 cur = conn.cursor()
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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399 results = cur.execute(query)
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400 if not options.no_header:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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401 outputFile.write("#%s\n" % '\t'.join([str(col[0]) for col in cur.description]))
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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402 # yield [col[0] for col in cur.description]
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403 for i, row in enumerate(results):
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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404 # yield [val for val in row]
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405 outputFile.write("%s\n" % '\t'.join([str(val) if val is not None else '' for val in row]))
0
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406 except Exception, exc:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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407 print >> sys.stderr, "Error: %s" % exc
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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408 exit(1)
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
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409
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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410 if __name__ == "__main__":
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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411 __main__()