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1 import os
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2 import argparse
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3 import sys
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4 import string
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5 import sqlite3
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6
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7 import logging
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8
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9
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10 class CummerbundParser(object):
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11
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12 def __init__(self, opts):
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13 self.cummerbund_db = opts.filename
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14 self.session = sqlite3.connect( os.path.abspath( self.cummerbund_db ) )
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15
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16 def generate_file( self, table ):
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17 if hasattr( self, table ):
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18 with open( '%s.tabular' % table, 'w' ) as self.fh:
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19 getattr( self, table )()
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20 else:
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21 print 'Table %s is not supported or does not exist.' % table
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22
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23 def __write_line(self, line):
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24 columns = []
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25 for col in line:
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26 if isinstance( col, float ):
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27 if str( col ) in [ '-inf', 'inf' ]:
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28 columns.append( str( col ) )
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29 elif col == int(col):
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30 columns.append( str( int( col ) ) )
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31 else:
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32 columns.append( str( col ) )
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33 elif col is None:
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34 columns.append( '-' )
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35 else:
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36 columns.append( str( col ) )
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37 print >>self.fh, '\t'.join( columns )
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38
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39 def __get_diff_from_table( self, table, identifier ):
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40 columns = [ '${table}.${identifier}', '${table}.gene_id', 'genes.gene_short_name', 'genes.locus',
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41 '${table}.sample_1', '${table}.sample_2', '${table}.status',
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42 '${table}.value_1', '${table}.value_2', '${table}.JS_dist',
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43 '${table}.test_stat', '${table}.p_value', '${table}.q_value',
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44 '${table}.significant' ]
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45 query = string.Template( 'SELECT %s FROM ${table} JOIN genes on ${table}.gene_id = genes.gene_id' % ', '.join(columns) )
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46 result = self.session.execute( query.safe_substitute( table=table, identifier=identifier ) )
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47 self.__write_line( [ 'test_id', 'gene_id', 'gene', 'locus', 'sample_1',
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48 'sample_2', 'status', 'value_1', 'value_2', 'sqrt(JS)',
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49 'test_stat', 'p_value', 'q_value', 'significant' ] )
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50 for row in result:
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51 self.__write_line( row )
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52
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53 def __get_read_group_data( self, table, identifier ):
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54 header = [ 'tracking_id', 'condition', 'replicate', 'raw_frags',
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55 'internal_scaled_frags', 'external_scaled_frags', 'FPKM',
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56 'effective_length', 'status' ]
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57 columns = [ identifier, 'sample_name', 'replicate', 'raw_frags',
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58 'internal_scaled_frags', 'external_scaled_frags', 'fpkm',
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59 'effective_length', 'status' ]
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60 self.__write_line( header )
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61 for row in self.session.execute( 'SELECT %s FROM %s' % ( ', '.join( columns ), table ) ):
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62 self.__write_line( row )
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63
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64
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65 def __get_exp_diff( self, table, data_table, data_table_as, column ):
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66 header = [ 'test_id', 'gene_id', 'gene', 'locus', 'sample_1', 'sample_2',
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67 'status', 'value_1', 'value_2', 'log2(fold_change)', 'test_stat',
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68 'p_value', 'q_value', 'significant' ]
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69 columns = [ '${dtas}.${column}', '${table}.gene_id', '${table}.gene_short_name', '${table}.locus',
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70 '${dtas}.sample_1', '${dtas}.sample_2', '${dtas}.status',
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71 '${dtas}.value_1', '${dtas}.value_2', '${dtas}.log2_fold_change',
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72 '${dtas}.test_stat', '${dtas}.p_value', '${dtas}.q_value',
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73 '${dtas}.significant' ]
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74 query = string.Template( 'SELECT %s FROM ${dtab} as ${dtas} JOIN ${table} on ${dtas}.${column} = ${table}.${column}' % ', '.join( columns ) )
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75 self.__write_line( header )
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76 for row in self.session.execute( query.safe_substitute( dtas=data_table_as, dtab=data_table, table=table, column=column ) ):
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77 self.__write_line( row )
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78
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79 def __get_per_sample_fpkm( self, identifiers, table, column ):
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80 columns = []
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81 for identifier in identifiers:
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82 samples = self.session.execute( "SELECT sample_name FROM %s WHERE %s = '%s' ORDER BY sample_name ASC" % ( table, column, identifier[0] ) )
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83 for sample in samples:
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84 sample_name = sample[0]
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85 columns.extend( [ '%s_FPKM' % sample_name,
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86 '%s_conf_lo' % sample_name,
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87 '%s_conf_hi' % sample_name,
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88 '%s_status' % sample_name ] )
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89 return columns
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90
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91 def __get_fpkms( self, table, data_table, column ):
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92 tss_columns = [ column, 'class_code', 'nearest_ref_id', 'gene_id',
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93 'gene_short_name', column, 'locus', 'length', 'coverage' ]
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94 output_cols = [ 'tracking_id', 'class_code', 'nearest_ref_id', 'gene_id', 'gene_short_name',
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95 'tss_id', 'locus', 'length', 'coverage' ]
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96 tss_groups = self.session.execute( 'SELECT %s FROM %s LIMIT 1' % ( ', '.join( tss_columns ), table ) )
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97 output_cols.extend( self.__get_per_sample_fpkm( identifiers=tss_groups, column=column, table=data_table ) )
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98 self.__write_line( output_cols )
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99 tss_groups = self.session.execute( 'SELECT %s FROM %s' % ( ', '.join( tss_columns ), table ) )
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100 for tss_group in tss_groups:
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101 out_data = list( tss_group )
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102 samples = self.session.execute( "SELECT fpkm, conf_hi, conf_lo, quant_status FROM %s WHERE %s = '%s' ORDER BY sample_name ASC" % ( data_table, column, tss_group[0] ) )
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103 for sample in samples:
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104 out_data.extend( list( sample ) )
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105 self.__write_line( out_data )
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106
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107 def __get_count_data( self, table, column ):
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108 output_cols = [ 'tracking_id' ]
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109 tss_groups = self.session.execute( 'SELECT %s FROM %s LIMIT 1' % ( column, table ) )
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110 output_cols.extend( self.__get_per_sample_count_cols( identifiers=tss_groups, table=table, column=column ) )
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111 self.__write_line( output_cols )
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112 self.__get_per_sample_count_data( table=table, column=column )
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113
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114 def __get_per_sample_count_data( self, table, column ):
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115 result = self.session.execute( 'SELECT DISTINCT(%s) FROM %s' % ( column, table ) )
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116 for row in result:
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117 isoform_id = row[0]
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118 output_data = [ isoform_id ]
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119 per_sample = self.session.execute( "SELECT count, variance, uncertainty, dispersion, status FROM %s WHERE %s = '%s' ORDER BY sample_name ASC" % ( table, column, isoform_id ) )
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120 for samplerow in per_sample:
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121 output_data.extend( list( samplerow ) )
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122 self.__write_line( output_data )
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123
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124 def __get_per_sample_count_cols( self, identifiers, table, column ):
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125 columns = []
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126 for identifier in identifiers:
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127 samples = self.session.execute( "SELECT sample_name FROM %s WHERE %s = '%s' ORDER BY sample_name ASC" % ( table, column, identifier[0] ) )
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128 for sample in samples:
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129 sample_name = sample[0]
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130 columns.extend( [ '%s_count' % sample_name,
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131 '%s_count_variance' % sample_name,
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132 '%s_count_uncertainty_var' % sample_name,
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133 '%s_count_dispersion_var' % sample_name,
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134 '%s_status' % sample_name ] )
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135 return columns
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136
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137 def splicing_diff( self ):
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138 self.__get_diff_from_table( 'splicingDiffData', 'TSS_group_id' )
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139
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140 def promoters_diff( self ):
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141 self.__get_diff_from_table( 'promoterDiffData', 'gene_id' )
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142
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143 def cds_diff( self ):
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144 self.__get_diff_from_table( 'CDSDiffData', 'gene_id' )
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145
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146 def tss_fpkm( self ):
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147 data_table = 'TSSData'
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148 table = 'TSS'
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149 column = 'TSS_group_id'
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150 self.__get_fpkms( data_table=data_table, table=table, column=column )
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151
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152 def isoform_fpkm( self ):
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153 data_table = 'isoformData'
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154 table = 'isoforms'
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155 column = 'isoform_id'
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156 self.__get_fpkms( data_table=data_table, table=table, column=column )
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157
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158 def genes_fpkm( self ):
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159 output_cols = [ 'tracking_id', 'class_code', 'nearest_ref_id', 'gene_id', 'gene_short_name',
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160 'tss_id', 'locus', 'length', 'coverage' ]
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161 iso_groups = self.session.execute( 'SELECT gene_id FROM genes LIMIT 1' )
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162 output_cols.extend( self.__get_per_sample_fpkm( identifiers=iso_groups, column='gene_id', table='geneData' ) )
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163 self.__write_line( output_cols )
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164 data_columns = [ 'genes.gene_id', 'genes.class_code', 'genes.nearest_ref_id', 'genes.gene_id', 'genes.gene_short_name',
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165 'GROUP_CONCAT(TSS.TSS_group_id)', 'genes.locus', 'genes.length', 'genes.coverage' ]
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166 query = 'SELECT %s FROM genes JOIN TSS on TSS.gene_id = genes.gene_id GROUP BY genes.gene_id' % ', '.join( data_columns )
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167 result = self.session.execute( query )
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168 for row in result:
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169 gene_id = row[0]
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170 output_data = list( row )
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171 per_sample = self.session.execute( "SELECT fpkm, conf_lo, conf_hi, quant_status FROM geneData WHERE gene_id = '%s' ORDER BY sample_name ASC" % gene_id )
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172 for samplerow in per_sample:
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173 output_data.extend( list( samplerow ) )
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174 self.__write_line( output_data )
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175
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176 def cds_fpkm( self ):
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177 output_cols = [ 'tracking_id', 'class_code', 'nearest_ref_id', 'gene_id', 'gene_short_name',
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178 'tss_id', 'locus', 'length', 'coverage' ]
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179 iso_groups = self.session.execute( 'SELECT CDS_id FROM CDS LIMIT 1' )
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180 output_cols.extend( self.__get_per_sample_fpkm( identifiers=iso_groups, column='CDS_id', table='CDSData' ) )
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181 self.__write_line( output_cols )
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182 data_columns = [ 'CDS_id', 'class_code', 'nearest_ref_id', 'gene_id', 'gene_short_name',
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183 'GROUP_CONCAT(TSS_group_id)', 'locus', 'length', 'coverage' ]
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184 query = 'SELECT %s FROM CDS GROUP BY CDS_id' % ', '.join( data_columns )
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185 result = self.session.execute( query )
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186 for row in result:
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187 CDS_id = row[0]
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188 output_data = list( row )
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189 per_sample = self.session.execute( "SELECT fpkm, conf_lo, conf_hi, quant_status FROM CDSData WHERE CDS_id = '%s' ORDER BY sample_name ASC" % CDS_id )
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190 for samplerow in per_sample:
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191 output_data.extend( list( samplerow ) )
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192 self.__write_line( output_data )
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193
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194 def tss_count_tracking( self ):
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195 self.__get_count_data( table='TSSCount', column='TSS_group_id' )
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196
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197 def isoform_count( self ):
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198 self.__get_count_data( table='isoformCount', column='isoform_id' )
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199
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200 def genes_count( self ):
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201 self.__get_count_data( table='geneCount', column='gene_id' )
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202
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203 def cds_count( self ):
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204 self.__get_count_data( table='CDSCount', column='CDS_id' )
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205
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206 def tss_group_exp( self ):
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207 columns = [ 'TEDD.TSS_group_id', 'TSS.gene_id', 'TSS.gene_short_name', 'TSS.locus',
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208 'TEDD.sample_1', 'TEDD.sample_2', 'TEDD.status',
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209 'TEDD.value_1', 'TEDD.value_2', 'TEDD.log2_fold_change',
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210 'TEDD.test_stat', 'TEDD.p_value', 'TEDD.q_value', 'TEDD.significant' ]
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211 query = [ 'SELECT %s FROM TSSExpDiffData AS TEDD' % ', '.join(columns),
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212 'JOIN TSS on TEDD.TSS_group_id = TSS.TSS_group_id' ]
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213 self.__write_line( [ 'test_id', 'gene_id', 'gene', 'locus',
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214 'sample_1', 'sample_2', 'status', 'value_1',
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215 'value_2', 'log2(fold_change)', 'test_stat',
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216 'p_value', 'q_value', 'significant' ] )
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217 for row in self.session.execute( ' '.join( query ) ):
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218 self.__write_line( row )
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219
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220 def run_info( self ):
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221 self.__write_line( [ 'param', 'value' ] )
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222 for row in self.session.execute( 'SELECT param, value FROM runInfo' ):
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223 self.__write_line( row )
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224
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225 def read_groups( self ):
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226 self.__write_line( [ 'file', 'condition', 'replicate_num', 'total_mass', 'norm_mass', 'internal_scale', 'external_scale' ] )
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227 for row in self.session.execute( 'SELECT file, sample_name, replicate, total_mass, norm_mass, internal_scale, external_scale FROM replicates' ):
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228 self.__write_line( row )
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229
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230 def isoform_exp_diff( self ):
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231 self.__get_exp_diff( table='isoforms', data_table='isoformExpDiffData', data_table_as='iED', column='isoform_id' )
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232
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233 def gene_exp_diff( self ):
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234 self.__get_exp_diff( table='genes', data_table='geneExpDiffData', data_table_as='gEDD', column='gene_id' )
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235
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236 def cds_exp_diff( self ):
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237 self.__get_exp_diff( table='CDS', data_table='CDSExpDiffData', data_table_as='CED', column='CDS_id' )
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238
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239 def tss_rg( self ):
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240 self.__get_read_group_data( table='TSSReplicateData', identifier='TSS_group_id' )
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241
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242 def isoform_rg( self ):
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243 self.__get_read_group_data( table='isoformReplicateData', identifier='isoform_id' )
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244
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245 def gene_rg( self ):
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246 self.__get_read_group_data( table='geneReplicateData', identifier='gene_id' )
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247
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248 def cds_rg( self ):
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249 self.__get_read_group_data( table='CDSReplicateData', identifier='CDS_id' )
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250
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251 def var_model( self ):
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252 header = [ 'condition', 'locus', 'compatible_count_mean', 'compatible_count_var', 'total_count_mean', 'total_count_var', 'fitted_var' ]
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253 self.__write_line( header )
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254 for row in self.session.execute( 'SELECT %s FROM varModel' % ', '.join( header ) ):
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255 self.__write_line( row )
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256
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257 if __name__ == '__main__':
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258 parser = argparse.ArgumentParser()
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259 parser.add_argument( '--file', dest='filename' )
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260 parser.add_argument( '--tables', dest='tables', action='append' )
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261 opts = parser.parse_args()
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262 cb = CummerbundParser( opts )
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263 for table in opts.tables:
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264 cb.generate_file( table )
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