# HG changeset patch # User devteam # Date 1428005617 14400 # Node ID 21d03c46f286df131f8c2d203a084b8cf77fa194 Uploaded diff -r 000000000000 -r 21d03c46f286 cummerbund_to_tabular.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cummerbund_to_tabular.py Thu Apr 02 16:13:37 2015 -0400 @@ -0,0 +1,264 @@ +import os +import argparse +import sys +import string +import sqlite3 + +import logging + + +class CummerbundParser(object): + + def __init__(self, opts): + self.cummerbund_db = opts.filename + self.session = sqlite3.connect( os.path.abspath( self.cummerbund_db ) ) + + def generate_file( self, table ): + if hasattr( self, table ): + with open( '%s.tabular' % table, 'w' ) as self.fh: + getattr( self, table )() + else: + print 'Table %s is not supported or does not exist.' % table + + def __write_line(self, line): + columns = [] + for col in line: + if isinstance( col, float ): + if str( col ) in [ '-inf', 'inf' ]: + columns.append( str( col ) ) + elif col == int(col): + columns.append( str( int( col ) ) ) + else: + columns.append( str( col ) ) + elif col is None: + columns.append( '-' ) + else: + columns.append( str( col ) ) + print >>self.fh, '\t'.join( columns ) + + def __get_diff_from_table( self, table, identifier ): + columns = [ '${table}.${identifier}', '${table}.gene_id', 'genes.gene_short_name', 'genes.locus', + '${table}.sample_1', '${table}.sample_2', '${table}.status', + '${table}.value_1', '${table}.value_2', '${table}.JS_dist', + '${table}.test_stat', '${table}.p_value', '${table}.q_value', + '${table}.significant' ] + query = string.Template( 'SELECT %s FROM ${table} JOIN genes on ${table}.gene_id = genes.gene_id' % ', '.join(columns) ) + result = self.session.execute( query.safe_substitute( table=table, identifier=identifier ) ) + self.__write_line( [ 'test_id', 'gene_id', 'gene', 'locus', 'sample_1', + 'sample_2', 'status', 'value_1', 'value_2', 'sqrt(JS)', + 'test_stat', 'p_value', 'q_value', 'significant' ] ) + for row in result: + self.__write_line( row ) + + def __get_read_group_data( self, table, identifier ): + header = [ 'tracking_id', 'condition', 'replicate', 'raw_frags', + 'internal_scaled_frags', 'external_scaled_frags', 'FPKM', + 'effective_length', 'status' ] + columns = [ identifier, 'sample_name', 'replicate', 'raw_frags', + 'internal_scaled_frags', 'external_scaled_frags', 'fpkm', + 'effective_length', 'status' ] + self.__write_line( header ) + for row in self.session.execute( 'SELECT %s FROM %s' % ( ', '.join( columns ), table ) ): + self.__write_line( row ) + + + def __get_exp_diff( self, table, data_table, data_table_as, column ): + header = [ 'test_id', 'gene_id', 'gene', 'locus', 'sample_1', 'sample_2', + 'status', 'value_1', 'value_2', 'log2(fold_change)', 'test_stat', + 'p_value', 'q_value', 'significant' ] + columns = [ '${dtas}.${column}', '${table}.gene_id', '${table}.gene_short_name', '${table}.locus', + '${dtas}.sample_1', '${dtas}.sample_2', '${dtas}.status', + '${dtas}.value_1', '${dtas}.value_2', '${dtas}.log2_fold_change', + '${dtas}.test_stat', '${dtas}.p_value', '${dtas}.q_value', + '${dtas}.significant' ] + query = string.Template( 'SELECT %s FROM ${dtab} as ${dtas} JOIN ${table} on ${dtas}.${column} = ${table}.${column}' % ', '.join( columns ) ) + self.__write_line( header ) + for row in self.session.execute( query.safe_substitute( dtas=data_table_as, dtab=data_table, table=table, column=column ) ): + self.__write_line( row ) + + def __get_per_sample_fpkm( self, identifiers, table, column ): + columns = [] + for identifier in identifiers: + samples = self.session.execute( "SELECT sample_name FROM %s WHERE %s = '%s' ORDER BY sample_name ASC" % ( table, column, identifier[0] ) ) + for sample in samples: + sample_name = sample[0] + columns.extend( [ '%s_FPKM' % sample_name, + '%s_conf_lo' % sample_name, + '%s_conf_hi' % sample_name, + '%s_status' % sample_name ] ) + return columns + + def __get_fpkms( self, table, data_table, column ): + tss_columns = [ column, 'class_code', 'nearest_ref_id', 'gene_id', + 'gene_short_name', column, 'locus', 'length', 'coverage' ] + output_cols = [ 'tracking_id', 'class_code', 'nearest_ref_id', 'gene_id', 'gene_short_name', + 'tss_id', 'locus', 'length', 'coverage' ] + tss_groups = self.session.execute( 'SELECT %s FROM %s LIMIT 1' % ( ', '.join( tss_columns ), table ) ) + output_cols.extend( self.__get_per_sample_fpkm( identifiers=tss_groups, column=column, table=data_table ) ) + self.__write_line( output_cols ) + tss_groups = self.session.execute( 'SELECT %s FROM %s' % ( ', '.join( tss_columns ), table ) ) + for tss_group in tss_groups: + out_data = list( tss_group ) + 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] ) ) + for sample in samples: + out_data.extend( list( sample ) ) + self.__write_line( out_data ) + + def __get_count_data( self, table, column ): + output_cols = [ 'tracking_id' ] + tss_groups = self.session.execute( 'SELECT %s FROM %s LIMIT 1' % ( column, table ) ) + output_cols.extend( self.__get_per_sample_count_cols( identifiers=tss_groups, table=table, column=column ) ) + self.__write_line( output_cols ) + self.__get_per_sample_count_data( table=table, column=column ) + + def __get_per_sample_count_data( self, table, column ): + result = self.session.execute( 'SELECT DISTINCT(%s) FROM %s' % ( column, table ) ) + for row in result: + isoform_id = row[0] + output_data = [ isoform_id ] + 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 ) ) + for samplerow in per_sample: + output_data.extend( list( samplerow ) ) + self.__write_line( output_data ) + + def __get_per_sample_count_cols( self, identifiers, table, column ): + columns = [] + for identifier in identifiers: + samples = self.session.execute( "SELECT sample_name FROM %s WHERE %s = '%s' ORDER BY sample_name ASC" % ( table, column, identifier[0] ) ) + for sample in samples: + sample_name = sample[0] + columns.extend( [ '%s_count' % sample_name, + '%s_count_variance' % sample_name, + '%s_count_uncertainty_var' % sample_name, + '%s_count_dispersion_var' % sample_name, + '%s_status' % sample_name ] ) + return columns + + def splicing_diff( self ): + self.__get_diff_from_table( 'splicingDiffData', 'TSS_group_id' ) + + def promoters_diff( self ): + self.__get_diff_from_table( 'promoterDiffData', 'gene_id' ) + + def cds_diff( self ): + self.__get_diff_from_table( 'CDSDiffData', 'gene_id' ) + + def tss_fpkm( self ): + data_table = 'TSSData' + table = 'TSS' + column = 'TSS_group_id' + self.__get_fpkms( data_table=data_table, table=table, column=column ) + + def isoform_fpkm( self ): + data_table = 'isoformData' + table = 'isoforms' + column = 'isoform_id' + self.__get_fpkms( data_table=data_table, table=table, column=column ) + + def genes_fpkm( self ): + output_cols = [ 'tracking_id', 'class_code', 'nearest_ref_id', 'gene_id', 'gene_short_name', + 'tss_id', 'locus', 'length', 'coverage' ] + iso_groups = self.session.execute( 'SELECT gene_id FROM genes LIMIT 1' ) + output_cols.extend( self.__get_per_sample_fpkm( identifiers=iso_groups, column='gene_id', table='geneData' ) ) + self.__write_line( output_cols ) + data_columns = [ 'genes.gene_id', 'genes.class_code', 'genes.nearest_ref_id', 'genes.gene_id', 'genes.gene_short_name', + 'GROUP_CONCAT(TSS.TSS_group_id)', 'genes.locus', 'genes.length', 'genes.coverage' ] + query = 'SELECT %s FROM genes JOIN TSS on TSS.gene_id = genes.gene_id GROUP BY genes.gene_id' % ', '.join( data_columns ) + result = self.session.execute( query ) + for row in result: + gene_id = row[0] + output_data = list( row ) + 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 ) + for samplerow in per_sample: + output_data.extend( list( samplerow ) ) + self.__write_line( output_data ) + + def cds_fpkm( self ): + output_cols = [ 'tracking_id', 'class_code', 'nearest_ref_id', 'gene_id', 'gene_short_name', + 'tss_id', 'locus', 'length', 'coverage' ] + iso_groups = self.session.execute( 'SELECT CDS_id FROM CDS LIMIT 1' ) + output_cols.extend( self.__get_per_sample_fpkm( identifiers=iso_groups, column='CDS_id', table='CDSData' ) ) + self.__write_line( output_cols ) + data_columns = [ 'CDS_id', 'class_code', 'nearest_ref_id', 'gene_id', 'gene_short_name', + 'GROUP_CONCAT(TSS_group_id)', 'locus', 'length', 'coverage' ] + query = 'SELECT %s FROM CDS GROUP BY CDS_id' % ', '.join( data_columns ) + result = self.session.execute( query ) + for row in result: + CDS_id = row[0] + output_data = list( row ) + 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 ) + for samplerow in per_sample: + output_data.extend( list( samplerow ) ) + self.__write_line( output_data ) + + def tss_count_tracking( self ): + self.__get_count_data( table='TSSCount', column='TSS_group_id' ) + + def isoform_count( self ): + self.__get_count_data( table='isoformCount', column='isoform_id' ) + + def genes_count( self ): + self.__get_count_data( table='geneCount', column='gene_id' ) + + def cds_count( self ): + self.__get_count_data( table='CDSCount', column='CDS_id' ) + + def tss_group_exp( self ): + columns = [ 'TEDD.TSS_group_id', 'TSS.gene_id', 'TSS.gene_short_name', 'TSS.locus', + 'TEDD.sample_1', 'TEDD.sample_2', 'TEDD.status', + 'TEDD.value_1', 'TEDD.value_2', 'TEDD.log2_fold_change', + 'TEDD.test_stat', 'TEDD.p_value', 'TEDD.q_value', 'TEDD.significant' ] + query = [ 'SELECT %s FROM TSSExpDiffData AS TEDD' % ', '.join(columns), + 'JOIN TSS on TEDD.TSS_group_id = TSS.TSS_group_id' ] + self.__write_line( [ 'test_id', 'gene_id', 'gene', 'locus', + 'sample_1', 'sample_2', 'status', 'value_1', + 'value_2', 'log2(fold_change)', 'test_stat', + 'p_value', 'q_value', 'significant' ] ) + for row in self.session.execute( ' '.join( query ) ): + self.__write_line( row ) + + def run_info( self ): + self.__write_line( [ 'param', 'value' ] ) + for row in self.session.execute( 'SELECT param, value FROM runInfo' ): + self.__write_line( row ) + + def read_groups( self ): + self.__write_line( [ 'file', 'condition', 'replicate_num', 'total_mass', 'norm_mass', 'internal_scale', 'external_scale' ] ) + for row in self.session.execute( 'SELECT file, sample_name, replicate, total_mass, norm_mass, internal_scale, external_scale FROM replicates' ): + self.__write_line( row ) + + def isoform_exp_diff( self ): + self.__get_exp_diff( table='isoforms', data_table='isoformExpDiffData', data_table_as='iED', column='isoform_id' ) + + def gene_exp_diff( self ): + self.__get_exp_diff( table='genes', data_table='geneExpDiffData', data_table_as='gEDD', column='gene_id' ) + + def cds_exp_diff( self ): + self.__get_exp_diff( table='CDS', data_table='CDSExpDiffData', data_table_as='CED', column='CDS_id' ) + + def tss_rg( self ): + self.__get_read_group_data( table='TSSReplicateData', identifier='TSS_group_id' ) + + def isoform_rg( self ): + self.__get_read_group_data( table='isoformReplicateData', identifier='isoform_id' ) + + def gene_rg( self ): + self.__get_read_group_data( table='geneReplicateData', identifier='gene_id' ) + + def cds_rg( self ): + self.__get_read_group_data( table='CDSReplicateData', identifier='CDS_id' ) + + def var_model( self ): + header = [ 'condition', 'locus', 'compatible_count_mean', 'compatible_count_var', 'total_count_mean', 'total_count_var', 'fitted_var' ] + self.__write_line( header ) + for row in self.session.execute( 'SELECT %s FROM varModel' % ', '.join( header ) ): + self.__write_line( row ) + +if __name__ == '__main__': + parser = argparse.ArgumentParser() + parser.add_argument( '--file', dest='filename' ) + parser.add_argument( '--tables', dest='tables', action='append' ) + opts = parser.parse_args() + cb = CummerbundParser( opts ) + for table in opts.tables: + cb.generate_file( table ) diff -r 000000000000 -r 21d03c46f286 cummerbund_to_tabular.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cummerbund_to_tabular.xml Thu Apr 02 16:13:37 2015 -0400 @@ -0,0 +1,244 @@ + + + tabular files from a cummeRbund database + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ('--tables cds_count' in tables) + + + ('--tables cds_diff' in tables) + + + ('--tables cds_exp_diff' in tables) + + + ('--tables cds_fpkm' in tables) + + + ('--tables cds_rg' in tables) + + + ('--tables gene_exp_diff' in tables) + + + ('--tables genes_count' in tables) + + + ('--tables genes_fpkm' in tables) + + + ('--tables gene_rg' in tables) + + + ('--tables isoform_exp_diff' in tables) + + + ('--tables isoform_count' in tables) + + + ('--tables isoform_fpkm' in tables) + + + ('--tables isoform_rg' in tables) + + + ('--tables promoters_diff' in tables) + + + ('--tables read_groups' in tables) + + + ('--tables run_info' in tables) + + + ('--tables splicing_diff' in tables) + + + ('--tables tss_group_exp' in tables) + + + ('--tables tss_count_tracking' in tables) + + + ('--tables tss_fpkm' in tables) + + + ('--tables tss_rg' in tables) + + + ('--tables var_model' in tables) + + + + doi:10.1038/nprot.2012.016 + + This tool extracts cuffdiff tabular files from a cummeRbund SQLite database. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r 21d03c46f286 test-data/cds_count.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cds_count.tabular Thu Apr 02 16:13:37 2015 -0400 @@ -0,0 +1,1 @@ +tracking_id diff -r 000000000000 -r 21d03c46f286 test-data/cds_diff.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cds_diff.tabular Thu Apr 02 16:13:37 2015 -0400 @@ -0,0 +1,1 @@ +test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant diff -r 000000000000 -r 21d03c46f286 test-data/cds_exp_diff.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cds_exp_diff.tabular Thu Apr 02 16:13:37 2015 -0400 @@ -0,0 +1,1 @@ +test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant diff -r 000000000000 -r 21d03c46f286 test-data/cds_fpkm.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cds_fpkm.tabular Thu Apr 02 16:13:37 2015 -0400 @@ -0,0 +1,1 @@ +tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage diff -r 000000000000 -r 21d03c46f286 test-data/cds_rg.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cds_rg.tabular Thu Apr 02 16:13:37 2015 -0400 @@ -0,0 +1,1 @@ +tracking_id condition replicate raw_frags internal_scaled_frags external_scaled_frags FPKM effective_length status diff -r 000000000000 -r 21d03c46f286 test-data/cuffdiff_out.sqlite Binary file test-data/cuffdiff_out.sqlite has changed diff -r 000000000000 -r 21d03c46f286 test-data/gene_exp_diff.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_exp_diff.tabular Thu Apr 02 16:13:37 2015 -0400 @@ -0,0 +1,88 @@ +test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant +XLOC_000001 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 OK 0 9459860 inf - 0.01975 0.09875 no +XLOC_000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 243637000 inf - 0.12465 0.181781 no +XLOC_000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000004 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000005 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000006 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000007 XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 358326 522345 0.543731 1.1445 0.1952 0.27328 no +XLOC_000008 XLOC_000008 - chr1:3190858-3191434 q1 q2 OK 408511 420354 0.0412311 0.0469899 0.96715 0.96715 no +XLOC_000009 XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 433286 842157 0.958769 1.27887 0.20385 0.274413 no +XLOC_000010 XLOC_000010 - chr1:3192250-3192336 q1 q2 OK 3441510 3344550 -0.0412311 -0.014084 0.67715 0.718189 no +XLOC_000011 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 97002000 inf - 0.07975 0.181781 no +XLOC_000012 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 4729930 inf - 0.12465 0.181781 no +XLOC_000013 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000014 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000015 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 6863860 inf - 0.0612 0.181781 no +XLOC_000016 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 243637000 inf - 0.12465 0.181781 no +XLOC_000017 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000018 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000019 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000020 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000021 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000022 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000023 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000024 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000025 XLOC_000025 - chr1:3200022-3200191 q1 q2 OK 826392 803108 -0.0412311 -0.0180163 0.8625 0.887868 no +XLOC_000026 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000027 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000028 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000029 XLOC_000029 - chr1:3201077-3201481 q1 q2 OK 66791.3 324548 2.2807 1.1905 0.3026 0.383188 no +XLOC_000030 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 16359000 0 -inf - 0.0148 0.09875 no +XLOC_000031 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000032 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 15136000 0 -inf - 0.06005 0.181781 no +XLOC_000033 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000034 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 OK 0 9459860 inf - 0.01975 0.09875 no +XLOC_000035 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 OK 0 28083700 inf - 0.0612 0.181781 no +XLOC_000036 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 OK 3784000 0 -inf - 0.12165 0.181781 no +XLOC_000037 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 OK 5107810 2082090 -1.29467 -0.482193 0.5916 0.647062 no +XLOC_000038 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000039 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000040 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 OK 48522.7 424400 3.12869 1.23747 0.38685 0.450823 no +XLOC_000041 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000042 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 OK 0 30305300 inf - 0.01975 0.09875 no +XLOC_000043 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 OK 86160000 0 -inf - 0.12165 0.181781 no +XLOC_000044 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 OK 0 57999100 inf - 0.01975 0.09875 no +XLOC_000045 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000046 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 OK 0 2354230000 inf - 0.01975 0.09875 no +XLOC_000047 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000048 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000049 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 OK 228872 47662.2 -2.26362 -1.16262 0.30655 0.383188 no +XLOC_000050 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000051 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000052 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 OK 0 26133400 inf - 0.12465 0.181781 no +XLOC_000053 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000054 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000055 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000056 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000057 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 OK 0 11150300 inf - 0.12465 0.181781 no +XLOC_000058 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 OK 15591900 0 -inf - 0.12165 0.181781 no +XLOC_000059 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 OK 294879 85971.3 -1.7782 -0.902752 0.36915 0.445526 no +XLOC_000060 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 OK 807732 156995 -2.36316 -0.89463 0.3993 0.450823 no +XLOC_000061 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000062 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000063 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000064 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000065 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000066 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000067 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 OK 7681690 0 -inf - 0.12165 0.181781 no +XLOC_000068 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 OK 504790 0 -inf - 0.04565 0.181781 no +XLOC_000069 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 OK 102717000 0 -inf - 0.12165 0.181781 no +XLOC_000070 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 OK 3810010 0 -inf - 0.0148 0.09875 no +XLOC_000071 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000072 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 OK 55365400 0 -inf - 0.0773 0.181781 no +XLOC_000073 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000074 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 OK 62896600 0 -inf - 0.12165 0.181781 no +XLOC_000075 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000076 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000077 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000078 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000079 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000080 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000081 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000082 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000083 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000084 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000085 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000086 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000087 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no diff -r 000000000000 -r 21d03c46f286 test-data/gene_rg.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gene_rg.tabular Thu Apr 02 16:13:37 2015 -0400 @@ -0,0 +1,175 @@ +tracking_id condition replicate raw_frags internal_scaled_frags external_scaled_frags FPKM effective_length status +XLOC_000001 q1 0 0 0 0 0 - OK +XLOC_000001 q2 0 2 1.94365 1.94365 9459860 - OK +XLOC_000002 q1 0 0 0 0 0 - OK +XLOC_000002 q2 0 1 0.971825 0.971825 243637000 - OK +XLOC_000003 q1 0 0 0 0 0 - OK +XLOC_000003 q2 0 0 0 0 0 - OK +XLOC_000004 q1 0 0 0 0 0 - OK +XLOC_000004 q2 0 0 0 0 0 - OK +XLOC_000005 q1 0 0 0 0 0 - OK +XLOC_000005 q2 0 0 0 0 0 - OK +XLOC_000006 q1 0 0 0 0 0 - OK +XLOC_000006 q2 0 0 0 0 0 - OK +XLOC_000007 q1 0 62 62 62 358326 - OK +XLOC_000007 q2 0 93 90.3798 90.3798 522345 - OK +XLOC_000008 q1 0 34 34 34 408511 - OK +XLOC_000008 q2 0 36 34.9857 34.9857 420354 - OK +XLOC_000009 q1 0 35 35 35 433286 - OK +XLOC_000009 q2 0 70 68.0278 68.0278 842157 - OK +XLOC_000010 q1 0 1 1 1 3441510 - OK +XLOC_000010 q2 0 1 0.971825 0.971825 3344550 - OK +XLOC_000011 q1 0 0 0 0 0 - OK +XLOC_000011 q2 0 3 2.91548 2.91548 97002000 - OK +XLOC_000012 q1 0 0 0 0 0 - OK +XLOC_000012 q2 0 1 0.971825 0.971825 4729930 - OK +XLOC_000013 q1 0 0 0 0 0 - OK +XLOC_000013 q2 0 0 0 0 0 - OK +XLOC_000014 q1 0 0 0 0 0 - OK +XLOC_000014 q2 0 0 0 0 0 - OK +XLOC_000015 q1 0 0 0 0 0 - OK +XLOC_000015 q2 0 4 3.8873 3.8873 6863860 - OK +XLOC_000016 q1 0 0 0 0 0 - OK +XLOC_000016 q2 0 1 0.971825 0.971825 243637000 - OK +XLOC_000017 q1 0 0 0 0 0 - OK +XLOC_000017 q2 0 0 0 0 0 - OK +XLOC_000018 q1 0 0 0 0 0 - OK +XLOC_000018 q2 0 0 0 0 0 - OK +XLOC_000019 q1 0 0 0 0 0 - OK +XLOC_000019 q2 0 0 0 0 0 - OK +XLOC_000020 q1 0 0 0 0 0 - OK +XLOC_000020 q2 0 0 0 0 0 - OK +XLOC_000021 q1 0 0 0 0 0 - OK +XLOC_000021 q2 0 0 0 0 0 - OK +XLOC_000022 q1 0 0 0 0 0 - OK +XLOC_000022 q2 0 0 0 0 0 - OK +XLOC_000023 q1 0 0 0 0 0 - OK +XLOC_000023 q2 0 0 0 0 0 - OK +XLOC_000024 q1 0 0 0 0 0 - OK +XLOC_000024 q2 0 0 0 0 0 - OK +XLOC_000025 q1 0 3 3 3 826392 - OK +XLOC_000025 q2 0 3 2.91548 2.91548 803108 - OK +XLOC_000026 q1 0 0 0 0 0 - OK +XLOC_000026 q2 0 0 0 0 0 - OK +XLOC_000027 q1 0 0 0 0 0 - OK +XLOC_000027 q2 0 0 0 0 0 - OK +XLOC_000028 q1 0 0 0 0 0 - OK +XLOC_000028 q2 0 0 0 0 0 - OK +XLOC_000029 q1 0 3 3 3 66791.3 - OK +XLOC_000029 q2 0 15 14.5774 14.5774 324548 - OK +XLOC_000030 q1 0 2 2 2 16359000 - OK +XLOC_000030 q2 0 0 0 0 0 - OK +XLOC_000031 q1 0 0 0 0 0 - OK +XLOC_000031 q2 0 0 0 0 0 - OK +XLOC_000032 q1 0 4 4 4 15136000 - OK +XLOC_000032 q2 0 0 0 0 0 - OK +XLOC_000033 q1 0 0 0 0 0 - OK +XLOC_000033 q2 0 0 0 0 0 - OK +XLOC_000034 q1 0 0 0 0 0 - OK +XLOC_000034 q2 0 2 1.94365 1.94365 9459860 - OK +XLOC_000035 q1 0 0 0 0 0 - OK +XLOC_000035 q2 0 4 3.8873 3.8873 28083700 - OK +XLOC_000036 q1 0 1 1 1 3784000 - OK +XLOC_000036 q2 0 0 0 0 0 - OK +XLOC_000037 q1 0 3 3 3 5107810 - OK +XLOC_000037 q2 0 1 0.971825 0.971825 2082090 - OK +XLOC_000038 q1 0 0 0 0 0 - OK +XLOC_000038 q2 0 0 0 0 0 - OK +XLOC_000039 q1 0 0 0 0 0 - OK +XLOC_000039 q2 0 0 0 0 0 - OK +XLOC_000040 q1 0 1 1 1 48522.7 - OK +XLOC_000040 q2 0 9 8.74643 8.74643 424400 - OK +XLOC_000041 q1 0 0 0 0 0 - OK +XLOC_000041 q2 0 0 0 0 0 - OK +XLOC_000042 q1 0 0 0 0 0 - OK +XLOC_000042 q2 0 2 1.94365 1.94365 30305300 - OK +XLOC_000043 q1 0 1 1 1 86160000 - OK +XLOC_000043 q2 0 0 0 0 0 - OK +XLOC_000044 q1 0 0 0 0 0 - OK +XLOC_000044 q2 0 2 1.94365 1.94365 57999100 - OK +XLOC_000045 q1 0 0 0 0 0 - OK +XLOC_000045 q2 0 0 0 0 0 - OK +XLOC_000046 q1 0 0 0 0 0 - OK +XLOC_000046 q2 0 2 1.94365 1.94365 2354230000 - OK +XLOC_000047 q1 0 0 0 0 0 - OK +XLOC_000047 q2 0 0 0 0 0 - OK +XLOC_000048 q1 0 0 0 0 0 - OK +XLOC_000048 q2 0 0 0 0 0 - OK +XLOC_000049 q1 0 14 14 14 228872 - OK +XLOC_000049 q2 0 3 2.91548 2.91548 47662.2 - OK +XLOC_000050 q1 0 0 0 0 0 - OK +XLOC_000050 q2 0 0 0 0 0 - OK +XLOC_000051 q1 0 0 0 0 0 - OK +XLOC_000051 q2 0 0 0 0 0 - OK +XLOC_000052 q1 0 0 0 0 0 - OK +XLOC_000052 q2 0 1 0.971825 0.971825 26133400 - OK +XLOC_000053 q1 0 0 0 0 0 - OK +XLOC_000053 q2 0 0 0 0 0 - OK +XLOC_000054 q1 0 0 0 0 0 - OK +XLOC_000054 q2 0 0 0 0 0 - OK +XLOC_000055 q1 0 0 0 0 0 - OK +XLOC_000055 q2 0 0 0 0 0 - OK +XLOC_000056 q1 0 0 0 0 0 - OK +XLOC_000056 q2 0 0 0 0 0 - OK +XLOC_000057 q1 0 0 0 0 0 - OK +XLOC_000057 q2 0 1 0.971825 0.971825 11150300 - OK +XLOC_000058 q1 0 1 1 1 15591900 - OK +XLOC_000058 q2 0 0 0 0 0 - OK +XLOC_000059 q1 0 10 10 10 294879 - OK +XLOC_000059 q2 0 3 2.91548 2.91548 85971.3 - OK +XLOC_000060 q1 0 5 5 5 807732 - OK +XLOC_000060 q2 0 1 0.971825 0.971825 156995 - OK +XLOC_000061 q1 0 0 0 0 0 - OK +XLOC_000061 q2 0 0 0 0 0 - OK +XLOC_000062 q1 0 0 0 0 0 - OK +XLOC_000062 q2 0 0 0 0 0 - OK +XLOC_000063 q1 0 0 0 0 0 - OK +XLOC_000063 q2 0 0 0 0 0 - OK +XLOC_000064 q1 0 0 0 0 0 - OK +XLOC_000064 q2 0 0 0 0 0 - OK +XLOC_000065 q1 0 0 0 0 0 - OK +XLOC_000065 q2 0 0 0 0 0 - OK +XLOC_000066 q1 0 0 0 0 0 - OK +XLOC_000066 q2 0 0 0 0 0 - OK +XLOC_000067 q1 0 1 1 1 7681690 - OK +XLOC_000067 q2 0 0 0 0 0 - OK +XLOC_000068 q1 0 4 4 4 504790 - OK +XLOC_000068 q2 0 0 0 0 0 - OK +XLOC_000069 q1 0 1 1 1 102717000 - OK +XLOC_000069 q2 0 0 0 0 0 - OK +XLOC_000070 q1 0 2 2 2 3810010 - OK +XLOC_000070 q2 0 0 0 0 0 - OK +XLOC_000071 q1 0 0 0 0 0 - OK +XLOC_000071 q2 0 0 0 0 0 - OK +XLOC_000072 q1 0 3 3 3 55365400 - OK +XLOC_000072 q2 0 0 0 0 0 - OK +XLOC_000073 q1 0 0 0 0 0 - OK +XLOC_000073 q2 0 0 0 0 0 - OK +XLOC_000074 q1 0 1 1 1 62896600 - OK +XLOC_000074 q2 0 0 0 0 0 - OK +XLOC_000075 q1 0 0 0 0 0 - OK +XLOC_000075 q2 0 0 0 0 0 - OK +XLOC_000076 q1 0 0 0 0 0 - OK +XLOC_000076 q2 0 0 0 0 0 - OK +XLOC_000077 q1 0 0 0 0 0 - OK +XLOC_000077 q2 0 0 0 0 0 - OK +XLOC_000078 q1 0 0 0 0 0 - OK +XLOC_000078 q2 0 0 0 0 0 - OK +XLOC_000079 q1 0 0 0 0 0 - OK +XLOC_000079 q2 0 0 0 0 0 - OK +XLOC_000080 q1 0 0 0 0 0 - OK +XLOC_000080 q2 0 0 0 0 0 - OK +XLOC_000081 q1 0 0 0 0 0 - OK +XLOC_000081 q2 0 0 0 0 0 - OK +XLOC_000082 q1 0 0 0 0 0 - OK +XLOC_000082 q2 0 0 0 0 0 - OK +XLOC_000083 q1 0 0 0 0 0 - OK +XLOC_000083 q2 0 0 0 0 0 - OK +XLOC_000084 q1 0 0 0 0 0 - OK +XLOC_000084 q2 0 0 0 0 0 - OK +XLOC_000085 q1 0 0 0 0 0 - OK +XLOC_000085 q2 0 0 0 0 0 - OK +XLOC_000086 q1 0 0 0 0 0 - OK +XLOC_000086 q2 0 0 0 0 0 - OK +XLOC_000087 q1 0 0 0 0 0 - OK +XLOC_000087 q2 0 0 0 0 0 - OK diff -r 000000000000 -r 21d03c46f286 test-data/genes_count.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genes_count.tabular Thu Apr 02 16:13:37 2015 -0400 @@ -0,0 +1,88 @@ +tracking_id q1_count q1_count_variance q1_count_uncertainty_var q1_count_dispersion_var q1_status q2_count q2_count_variance q2_count_uncertainty_var q2_count_dispersion_var q2_status +XLOC_000001 0 0 0 0 OK 1.94365 6 0 5.96791 OK +XLOC_000002 0 0 0 0 OK 0.971825 2 0 1.66607 OK +XLOC_000003 0 0 0 0 OK 0 0 0 0 OK +XLOC_000004 0 0 0 0 OK 0 0 0 0 OK +XLOC_000005 0 0 0 0 OK 0 0 0 0 OK +XLOC_000006 0 0 0 0 OK 0 0 0 0 OK +XLOC_000007 62 373 0 372.146 OK 90.3798 93.159 0 90.3798 OK +XLOC_000008 34 217 0 216.229 OK 34.9857 223 0 222.222 OK +XLOC_000009 35 223 0 222.301 OK 68.0278 407.225 0 405.846 OK +XLOC_000010 1 2 0 1.78395 OK 0.971825 2 0 1.66607 OK +XLOC_000011 0 0 0 0 OK 2.91548 11 0 10.1281 OK +XLOC_000012 0 0 0 0 OK 0.971825 2 0 1.66607 OK +XLOC_000013 0 0 0 0 OK 0 0 0 0 OK +XLOC_000014 0 0 0 0 OK 0 0 0 0 OK +XLOC_000015 0 0 0 0 OK 3.8873 17 0 16.2636 OK +XLOC_000016 0 0 0 0 OK 0.971825 2 0 1.66607 OK +XLOC_000017 0 0 0 0 OK 0 0 0 0 OK +XLOC_000018 0 0 0 0 OK 0 0 0 0 OK +XLOC_000019 0 0 0 0 OK 0 0 0 0 OK +XLOC_000020 0 0 0 0 OK 0 0 0 0 OK +XLOC_000021 0 0 0 0 OK 0 0 0 0 OK +XLOC_000022 0 0 0 0 OK 0 0 0 0 OK +XLOC_000023 0 0 0 0 OK 0 0 0 0 OK +XLOC_000024 0 0 0 0 OK 0 0 0 0 OK +XLOC_000025 3 11 0 10.5107 OK 2.91548 11 0 10.1281 OK +XLOC_000026 0 0 0 0 OK 0 0 0 0 OK +XLOC_000027 0 0 0 0 OK 0 0 0 0 OK +XLOC_000028 0 0 0 0 OK 0 0 0 0 OK +XLOC_000029 3 11 0 10.5107 OK 14.5774 114.978 0 87.355 OK +XLOC_000030 2 7 0 6.18584 OK 0 0 0 0 OK +XLOC_000031 0 0 0 0 OK 0 0 0 0 OK +XLOC_000032 4 17 0 16.9943 OK 0 0 0 0 OK +XLOC_000033 0 0 0 0 OK 0 0 0 0 OK +XLOC_000034 0 0 0 0 OK 1.94365 6 0 5.96791 OK +XLOC_000035 0 0 0 0 OK 3.8873 17 0 16.2636 OK +XLOC_000036 1 2 0 1.78395 OK 0 0 0 0 OK +XLOC_000037 3 11.0603 0 10.5107 OK 0.971825 2.99194 0 1.66607 OK +XLOC_000038 0 0 0 0 OK 0 0 0 0 OK +XLOC_000039 0 0 0 0 OK 0 0 0 0 OK +XLOC_000040 1 2 0 1.78395 OK 8.74643 81.9454 0 48.6822 OK +XLOC_000041 0 0 0 0 OK 0 0 0 0 OK +XLOC_000042 0 0 0 0 OK 1.94365 6 0 5.96791 OK +XLOC_000043 1 2 0 1.78395 OK 0 0 0 0 OK +XLOC_000044 0 0 0 0 OK 1.94365 6 0 5.96791 OK +XLOC_000045 0 0 0 0 OK 0 0 0 0 OK +XLOC_000046 0 0 0 0 OK 1.94365 6 0 5.96791 OK +XLOC_000047 0 0 0 0 OK 0 0 0 0 OK +XLOC_000048 0 0 0 0 OK 0 0 0 0 OK +XLOC_000049 14 103.329 0 83.524 OK 2.91548 11 0 10.1281 OK +XLOC_000050 0 0 0 0 OK 0 0 0 0 OK +XLOC_000051 0 0 0 0 OK 0 0 0 0 OK +XLOC_000052 0 0 0 0 OK 0.971825 2 0 1.66607 OK +XLOC_000053 0 0 0 0 OK 0 0 0 0 OK +XLOC_000054 0 0 0 0 OK 0 0 0 0 OK +XLOC_000055 0 0 0 0 OK 0 0 0 0 OK +XLOC_000056 0 0 0 0 OK 0 0 0 0 OK +XLOC_000057 0 0 0 0 OK 0.971825 2 0 1.66607 OK +XLOC_000058 1 2 0 1.78395 OK 0 0 0 0 OK +XLOC_000059 10 57 0 56.983 OK 2.91548 11 0 10.1281 OK +XLOC_000060 5 24.9346 0 23.5132 OK 0.971825 2.99194 0 1.66607 OK +XLOC_000061 0 0 0 0 OK 0 0 0 0 OK +XLOC_000062 0 0 0 0 OK 0 0 0 0 OK +XLOC_000063 0 0 0 0 OK 0 0 0 0 OK +XLOC_000064 0 0 0 0 OK 0 0 0 0 OK +XLOC_000065 0 0 0 0 OK 0 0 0 0 OK +XLOC_000066 0 0 0 0 OK 0 0 0 0 OK +XLOC_000067 1 2 0 1.78395 OK 0 0 0 0 OK +XLOC_000068 4 17.9966 0 16.9943 OK 0 0 0 0 OK +XLOC_000069 1 2 0 1.78395 OK 0 0 0 0 OK +XLOC_000070 2 7 0 6.18584 OK 0 0 0 0 OK +XLOC_000071 0 0 0 0 OK 0 0 0 0 OK +XLOC_000072 3 11 0 10.5107 OK 0 0 0 0 OK +XLOC_000073 0 0 0 0 OK 0 0 0 0 OK +XLOC_000074 1 2 0 1.78395 OK 0 0 0 0 OK +XLOC_000075 0 0 0 0 OK 0 0 0 0 OK +XLOC_000076 0 0 0 0 OK 0 0 0 0 OK +XLOC_000077 0 0 0 0 OK 0 0 0 0 OK +XLOC_000078 0 0 0 0 OK 0 0 0 0 OK +XLOC_000079 0 0 0 0 OK 0 0 0 0 OK +XLOC_000080 0 0 0 0 OK 0 0 0 0 OK +XLOC_000081 0 0 0 0 OK 0 0 0 0 OK +XLOC_000082 0 0 0 0 OK 0 0 0 0 OK +XLOC_000083 0 0 0 0 OK 0 0 0 0 OK +XLOC_000084 0 0 0 0 OK 0 0 0 0 OK +XLOC_000085 0 0 0 0 OK 0 0 0 0 OK +XLOC_000086 0 0 0 0 OK 0 0 0 0 OK +XLOC_000087 0 0 0 0 OK 0 0 0 0 OK diff -r 000000000000 -r 21d03c46f286 test-data/genes_fpkm.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genes_fpkm.tabular Thu Apr 02 16:13:37 2015 -0400 @@ -0,0 +1,88 @@ +tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage q1_FPKM q1_conf_lo q1_conf_hi q1_status q2_FPKM q2_conf_lo q2_conf_hi q2_status +XLOC_000001 - - XLOC_000001 Xkr4 TSS1 chr1:3204754-3204833 - - 0 0 0 OK 9459860 0 33303500 OK +XLOC_000002 - - XLOC_000002 - TSS2 chr1:3111449-3111490 - - 0 0 0 OK 243637000 0 952723000 OK +XLOC_000003 - - XLOC_000003 - TSS3 chr1:3111545-3111576 - - 0 0 0 OK 0 0 0 OK +XLOC_000004 - - XLOC_000004 - TSS4 chr1:3174765-3174792 - - 0 0 0 OK 0 0 0 OK +XLOC_000005 - - XLOC_000005 - TSS5 chr1:3187401-3187428 - - 0 0 0 OK 0 0 0 OK +XLOC_000006 - - XLOC_000006 - TSS6 chr1:3188521-3188548 - - 0 0 0 OK 0 0 0 OK +XLOC_000007 - - XLOC_000007 - TSS7 chr1:3189810-3190789 - - 358326 135086 581565 OK 522345 410780 633911 OK +XLOC_000008 - - XLOC_000008 - TSS10 chr1:3190858-3191434 - - 408511 54526.1 762496 OK 420354 61509.1 779200 OK +XLOC_000009 - - XLOC_000009 - TSS11 chr1:3191512-3192077 - - 433286 63552.3 803020 OK 842157 342520 1341790 OK +XLOC_000010 - - XLOC_000010 - TSS13 chr1:3192250-3192336 - - 3441510 0 13175600 OK 3344550 0 13078600 OK +XLOC_000011 - - XLOC_000011 - TSS14 chr1:3192441-3192494 - - 0 0 0 OK 97002000 0 317699000 OK +XLOC_000012 - - XLOC_000012 - TSS15 chr1:3192550-3192629 - - 0 0 0 OK 4729930 0 18496100 OK +XLOC_000013 - - XLOC_000013 - TSS16 chr1:3192649-3192676 - - 0 0 0 OK 0 0 0 OK +XLOC_000014 - - XLOC_000014 - TSS17 chr1:3192731-3192811 - - 0 0 0 OK 0 0 0 OK +XLOC_000015 - - XLOC_000015 - TSS18 chr1:3192940-3193042 - - 0 0 0 OK 6863860 0 21424300 OK +XLOC_000016 - - XLOC_000016 - TSS19 chr1:3194185-3194226 - - 0 0 0 OK 243637000 0 952723000 OK +XLOC_000017 - - XLOC_000017 - TSS20 chr1:3194302-3194329 - - 0 0 0 OK 0 0 0 OK +XLOC_000018 - - XLOC_000018 - TSS21 chr1:3194706-3194733 - - 0 0 0 OK 0 0 0 OK +XLOC_000019 - - XLOC_000019 - TSS22 chr1:3195083-3195110 - - 0 0 0 OK 0 0 0 OK +XLOC_000020 - - XLOC_000020 - TSS23 chr1:3195450-3195477 - - 0 0 0 OK 0 0 0 OK +XLOC_000021 - - XLOC_000021 - TSS24 chr1:3197089-3197116 - - 0 0 0 OK 0 0 0 OK +XLOC_000022 - - XLOC_000022 - TSS25 chr1:3197246-3197273 - - 0 0 0 OK 0 0 0 OK +XLOC_000023 - - XLOC_000023 - TSS26 chr1:3197346-3197373 - - 0 0 0 OK 0 0 0 OK +XLOC_000024 - - XLOC_000024 - TSS27 chr1:3197425-3197452 - - 0 0 0 OK 0 0 0 OK +XLOC_000025 - - XLOC_000025 - TSS28 chr1:3200022-3200191 - - 826392 0 2653610 OK 803108 0 2630330 OK +XLOC_000026 - - XLOC_000026 - TSS29 chr1:3200325-3200352 - - 0 0 0 OK 0 0 0 OK +XLOC_000027 - - XLOC_000027 - TSS30 chr1:3200430-3200457 - - 0 0 0 OK 0 0 0 OK +XLOC_000028 - - XLOC_000028 - TSS31 chr1:3201007-3201039 - - 0 0 0 OK 0 0 0 OK +XLOC_000029 - - XLOC_000029 - TSS32 chr1:3201077-3201481 - - 66791.3 0 214473 OK 324548 0 802006 OK +XLOC_000030 - - XLOC_000030 - TSS33 chr1:3201596-3201666 - - 16359000 0 59640900 OK 0 0 0 OK +XLOC_000031 - - XLOC_000031 - TSS34 chr1:3201672-3201699 - - 0 0 0 OK 0 0 0 OK +XLOC_000032 - - XLOC_000032 - TSS35 chr1:3201725-3201809 - - 15136000 0 46339600 OK 0 0 0 OK +XLOC_000033 - - XLOC_000033 Xkr4 TSS36 chr1:3211521-3211561 - - 0 0 0 OK 0 0 0 OK +XLOC_000034 - - XLOC_000034 Xkr4 TSS37 chr1:3212213-3212292 - - 0 0 0 OK 9459860 0 33303500 OK +XLOC_000035 - - XLOC_000035 Xkr4 TSS38 chr1:3212367-3212439 - - 0 0 0 OK 28083700 0 87658400 OK +XLOC_000036 - - XLOC_000036 Xkr4 TSS39 chr1:3212717-3212801 - - 3784000 0 14486800 OK 0 0 0 OK +XLOC_000037 - - XLOC_000037 Xkr4 TSS40 chr1:3213095-3213242 - - 5107810 0 16958800 OK 2082090 0 8142100 OK +XLOC_000038 - - XLOC_000038 Xkr4 TSS41 chr1:3240606-3240633 - - 0 0 0 OK 0 0 0 OK +XLOC_000039 - - XLOC_000039 Xkr4 TSS42 chr1:3242479-3242512 - - 0 0 0 OK 0 0 0 OK +XLOC_000040 - - XLOC_000040 Xkr4 TSS43 chr1:3242633-3242923 - - 48522.7 0 185766 OK 424400 0 1302890 OK +XLOC_000041 - - XLOC_000041 Xkr4 TSS44 chr1:3242924-3243005 - - 0 0 0 OK 0 0 0 OK +XLOC_000042 - - XLOC_000042 Xkr4 TSS45 chr1:3243018-3243079 - - 0 0 0 OK 30305300 0 106690000 OK +XLOC_000043 - - XLOC_000043 Xkr4 TSS46 chr1:3243108-3243154 - - 86160000 0 329857000 OK 0 0 0 OK +XLOC_000044 - - XLOC_000044 Xkr4 TSS47 chr1:3243347-3243401 - - 0 0 0 OK 57999100 0 204186000 OK +XLOC_000045 - - XLOC_000045 Xkr4 TSS48 chr1:3254079-3254106 - - 0 0 0 OK 0 0 0 OK +XLOC_000046 - - XLOC_000046 Xkr4 TSS49 chr1:3256974-3257011 - - 0 0 0 OK 2354230000 0 8288060000 OK +XLOC_000047 - - XLOC_000047 Xkr4 TSS50 chr1:3277155-3277182 - - 0 0 0 OK 0 0 0 OK +XLOC_000048 - - XLOC_000048 Xkr4 TSS51 chr1:3277190-3277218 - - 0 0 0 OK 0 0 0 OK +XLOC_000049 - - XLOC_000049 Xkr4 TSS52 chr1:3277913-3278390 - - 228872 0 561229 OK 47662.2 0 156103 OK +XLOC_000050 - - XLOC_000050 Xkr4 TSS54 chr1:3280117-3280144 - - 0 0 0 OK 0 0 0 OK +XLOC_000051 - - XLOC_000051 Xkr4 TSS55 chr1:3280498-3280525 - - 0 0 0 OK 0 0 0 OK +XLOC_000052 - - XLOC_000052 Xkr4 TSS56 chr1:3280686-3280741 - - 0 0 0 OK 26133400 0 102193000 OK +XLOC_000053 - - XLOC_000053 Xkr4 TSS57 chr1:3282504-3282531 - - 0 0 0 OK 0 0 0 OK +XLOC_000054 - - XLOC_000054 Xkr4 TSS58 chr1:3282650-3282677 - - 0 0 0 OK 0 0 0 OK +XLOC_000055 - - XLOC_000055 Xkr4 TSS59 chr1:3282760-3282832 - - 0 0 0 OK 0 0 0 OK +XLOC_000056 - - XLOC_000056 Xkr4 TSS60 chr1:3284966-3284993 - - 0 0 0 OK 0 0 0 OK +XLOC_000057 - - XLOC_000057 Xkr4 TSS61 chr1:3290488-3290553 - - 0 0 0 OK 11150300 0 43602600 OK +XLOC_000058 - - XLOC_000058 Xkr4 TSS62 chr1:3290798-3290859 - - 15591900 0 59692600 OK 0 0 0 OK +XLOC_000059 - - XLOC_000059 Xkr4 TSS63 chr1:3290919-3291273 - - 294879 0 740137 OK 85971.3 0 281572 OK +XLOC_000060 - - XLOC_000060 Xkr4 TSS65,TSS66 chr1:3299443-3299664 - - 807732 0 2397860 OK 156995 0 641748 OK +XLOC_000061 - - XLOC_000061 Xkr4 TSS67 chr1:3299691-3299733 - - 0 0 0 OK 0 0 0 OK +XLOC_000062 - - XLOC_000062 Xkr4 TSS68 chr1:3300051-3300078 - - 0 0 0 OK 0 0 0 OK +XLOC_000063 - - XLOC_000063 Xkr4 TSS69 chr1:3307748-3307775 - - 0 0 0 OK 0 0 0 OK +XLOC_000064 - - XLOC_000064 Xkr4 TSS70 chr1:3318620-3318647 - - 0 0 0 OK 0 0 0 OK +XLOC_000065 - - XLOC_000065 Xkr4 TSS71 chr1:3318999-3319051 - - 0 0 0 OK 0 0 0 OK +XLOC_000066 - - XLOC_000066 Xkr4 TSS72 chr1:3330527-3330554 - - 0 0 0 OK 0 0 0 OK +XLOC_000067 - - XLOC_000067 Xkr4 TSS73 chr1:3351240-3351311 - - 7681690 0 29408800 OK 0 0 0 OK +XLOC_000068 - - XLOC_000068 Xkr4 TSS74 chr1:3355887-3356119 - - 504790 0 1597120 OK 0 0 0 OK +XLOC_000069 - - XLOC_000069 Xkr4 TSS75 chr1:3356180-3356225 - - 102717000 0 393246000 OK 0 0 0 OK +XLOC_000070 - - XLOC_000070 Xkr4 TSS76 chr1:3363076-3363176 - - 3810010 0 13890300 OK 0 0 0 OK +XLOC_000071 - - XLOC_000071 Xkr4 TSS77 chr1:3363214-3363278 - - 0 0 0 OK 0 0 0 OK +XLOC_000072 - - XLOC_000072 Xkr4 TSS78 chr1:3363387-3363446 - - 55365400 0 177783000 OK 0 0 0 OK +XLOC_000073 - - XLOC_000073 Xkr4 TSS79 chr1:3363753-3363849 - - 0 0 0 OK 0 0 0 OK +XLOC_000074 - - XLOC_000074 Xkr4 TSS80 chr1:3364871-3364919 - - 62896600 0 240795000 OK 0 0 0 OK +XLOC_000075 - - XLOC_000075 Xkr4 TSS81 chr1:3367135-3367162 - - 0 0 0 OK 0 0 0 OK +XLOC_000076 - - XLOC_000076 Xkr4 TSS82 chr1:3367210-3367237 - - 0 0 0 OK 0 0 0 OK +XLOC_000077 - - XLOC_000077 Xkr4 TSS83 chr1:3367333-3367382 - - 0 0 0 OK 0 0 0 OK +XLOC_000078 - - XLOC_000078 Xkr4 TSS84 chr1:3369580-3369607 - - 0 0 0 OK 0 0 0 OK +XLOC_000079 - - XLOC_000079 Xkr4 TSS85 chr1:3375001-3375028 - - 0 0 0 OK 0 0 0 OK +XLOC_000080 - - XLOC_000080 Xkr4 TSS86 chr1:3377211-3377262 - - 0 0 0 OK 0 0 0 OK +XLOC_000081 - - XLOC_000081 Xkr4 TSS87 chr1:3379888-3379915 - - 0 0 0 OK 0 0 0 OK +XLOC_000082 - - XLOC_000082 Xkr4 TSS88 chr1:3386739-3386836 - - 0 0 0 OK 0 0 0 OK +XLOC_000083 - - XLOC_000083 Xkr4 TSS89 chr1:3391325-3391352 - - 0 0 0 OK 0 0 0 OK +XLOC_000084 - - XLOC_000084 Xkr4 TSS90 chr1:3435841-3435880 - - 0 0 0 OK 0 0 0 OK +XLOC_000085 - - XLOC_000085 Xkr4 TSS91 chr1:3447761-3447788 - - 0 0 0 OK 0 0 0 OK +XLOC_000086 - - XLOC_000086 Xkr4 TSS92 chr1:3450906-3450965 - - 0 0 0 OK 0 0 0 OK +XLOC_000087 - - XLOC_000087 Xkr4 TSS93 chr1:3451051-3451109 - - 0 0 0 OK 0 0 0 OK diff -r 000000000000 -r 21d03c46f286 test-data/isoform_count.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/isoform_count.tabular Thu Apr 02 16:13:37 2015 -0400 @@ -0,0 +1,91 @@ +tracking_id q1_count q1_count_variance q1_count_uncertainty_var q1_count_dispersion_var q1_status q2_count q2_count_variance q2_count_uncertainty_var q2_count_dispersion_var q2_status +TCONS_00000001 0 0 0 0 OK 1.94365 6 0 5.96791 OK +TCONS_00000002 0 0 0 0 OK 0.971825 2 0 1.66607 OK +TCONS_00000003 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000009 0 0 0 0 OK 2.91548 11 0 10.1281 OK +TCONS_00000010 0 0 0 0 OK 0.971825 2 0 1.66607 OK +TCONS_00000011 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000012 0 0 0 0 OK 3.8873 17 0 16.2636 OK +TCONS_00000013 0 0 0 0 OK 0.971825 2 0 1.66607 OK +TCONS_00000014 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000015 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000016 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000017 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000018 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000019 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000020 3 11 0 10.5107 OK 2.91548 11 0 10.1281 OK +TCONS_00000021 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000022 3 11 0 10.5107 OK 14.5774 114.978 0 87.355 OK +TCONS_00000023 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000024 0 0 0 0 OK 1.94365 6 0 5.96791 OK +TCONS_00000025 0 0 0 0 OK 3.8873 17 0 16.2636 OK +TCONS_00000026 1.9812 7 0 6.94124 OK 0.971825 2 0 1.66607 OK +TCONS_00000027 1 2 0 1.78395 OK 8.74643 81.9454 0 48.6822 OK +TCONS_00000028 0 0 0 0 OK 1.94365 6 0 5.96791 OK +TCONS_00000029 0 0 0 0 OK 1.94365 6 0 5.96791 OK +TCONS_00000030 0 0 0 0 OK 1.94365 6 0 5.96791 OK +TCONS_00000031 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000033 0 0 0 0 OK 0.971825 2 0 1.66607 OK +TCONS_00000034 0 0 0 0 OK 0.971825 2 0 1.66607 OK +TCONS_00000037 0 1 0 0 OK 0 1 0 0 OK +TCONS_00000038 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000039 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000040 0 1 0 0 OK 0 0 0 0 OK +TCONS_00000041 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000042 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000043 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000044 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000045 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000046 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000047 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000048 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000049 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000050 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000051 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000052 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000053 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000054 62 373 0 372.146 OK 90.3798 93.159 0 90.3798 OK +TCONS_00000055 34 217 0 216.229 OK 34.9857 223 0 222.222 OK +TCONS_00000056 35 223 0 222.301 OK 68.0278 407.225 0 405.846 OK +TCONS_00000057 1 2 0 1.78395 OK 0.971825 2 0 1.66607 OK +TCONS_00000058 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000059 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000060 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000062 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000063 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000065 2 7 0 6.18584 OK 0 0 0 0 OK +TCONS_00000066 4 17 0 16.9943 OK 0 0 0 0 OK +TCONS_00000067 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000068 1 2 0 1.78395 OK 0 0 0 0 OK +TCONS_00000069 1.0188 4 0 3.56944 OK 0 1 0 0 OK +TCONS_00000070 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000071 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000072 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000073 1 2 0 1.78395 OK 0 0 0 0 OK +TCONS_00000074 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000075 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000076 14 103.329 0 83.524 OK 2.91548 11 0 10.1281 OK +TCONS_00000077 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000078 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000079 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000080 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000081 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000082 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000083 1 2 0 1.78395 OK 0 0 0 0 OK +TCONS_00000084 10 57 0 56.983 OK 2.91548 11 0 10.1281 OK +TCONS_00000085 5 24 0 23.5132 OK 0.971825 2 0 1.66607 OK +TCONS_00000086 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000087 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000088 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000089 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000090 1 2 0 1.78395 OK 0 0 0 0 OK +TCONS_00000091 4 17 0 16.9943 OK 0 0 0 0 OK +TCONS_00000092 1 2 0 1.78395 OK 0 0 0 0 OK +TCONS_00000093 2 7 0 6.18584 OK 0 0 0 0 OK +TCONS_00000094 3 11 0 10.5107 OK 0 0 0 0 OK +TCONS_00000095 1 2 0 1.78395 OK 0 0 0 0 OK +TCONS_00000096 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000097 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000098 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000099 0 0 0 0 OK 0 0 0 0 OK +TCONS_00000100 0 0 0 0 OK 0 0 0 0 OK diff -r 000000000000 -r 21d03c46f286 test-data/isoform_exp_diff.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/isoform_exp_diff.tabular Thu Apr 02 16:13:37 2015 -0400 @@ -0,0 +1,91 @@ +test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant +TCONS_00000001 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 OK 0 9459860 inf - 0.01975 0.101571 no +TCONS_00000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 243637000 inf - 0.12465 0.186975 no +TCONS_00000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000009 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 97002000 inf - 0.07975 0.186975 no +TCONS_00000010 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 4729930 inf - 0.12465 0.186975 no +TCONS_00000011 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000012 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 6863860 inf - 0.0612 0.186975 no +TCONS_00000013 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 243637000 inf - 0.12465 0.186975 no +TCONS_00000014 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000015 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000016 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000017 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000018 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000019 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000020 XLOC_000025 - chr1:3200022-3200191 q1 q2 OK 826392 803108 -0.0412311 -0.0180163 0.8625 0.887143 no +TCONS_00000021 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000022 XLOC_000029 - chr1:3201077-3201481 q1 q2 OK 66791.3 324548 2.2807 1.1905 0.3026 0.380545 no +TCONS_00000023 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000024 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 OK 0 9459860 inf - 0.01975 0.101571 no +TCONS_00000025 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 OK 0 28083700 inf - 0.0612 0.186975 no +TCONS_00000026 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 OK 4244630 2082090 -1.0276 -0.36063 0.3844 0.435206 no +TCONS_00000027 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 OK 48522.7 424400 3.12869 1.23747 0.38685 0.435206 no +TCONS_00000028 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 OK 0 30305300 inf - 0.01975 0.101571 no +TCONS_00000029 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 OK 0 57999100 inf - 0.01975 0.101571 no +TCONS_00000030 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 OK 0 2354230000 inf - 0.01975 0.101571 no +TCONS_00000031 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000033 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 OK 0 26133400 inf - 0.12465 0.186975 no +TCONS_00000034 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 OK 0 11150300 inf - 0.12465 0.186975 no +TCONS_00000037 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000038 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000039 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000040 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000041 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000042 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000043 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000044 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000045 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000046 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000047 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000048 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000049 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000050 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000051 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000052 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000053 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000054 XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 358326 522345 0.543731 1.1445 0.1952 0.270969 no +TCONS_00000055 XLOC_000008 - chr1:3190858-3191434 q1 q2 OK 408511 420354 0.0412311 0.0469899 0.96715 0.96715 no +TCONS_00000056 XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 433286 842157 0.958769 1.27887 0.20385 0.2718 no +TCONS_00000057 XLOC_000010 - chr1:3192250-3192336 q1 q2 OK 3441510 3344550 -0.0412311 -0.014084 0.67715 0.716982 no +TCONS_00000058 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000059 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000060 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000062 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000063 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000065 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 16359000 0 -inf - 0.0148 0.101571 no +TCONS_00000066 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 15136000 0 -inf - 0.06005 0.186975 no +TCONS_00000067 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000068 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 OK 3784000 0 -inf - 0.12165 0.186975 no +TCONS_00000069 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 OK 863189 0 -inf - 0.1957 0.270969 no +TCONS_00000070 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000071 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000072 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000073 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 OK 86160000 0 -inf - 0.12165 0.186975 no +TCONS_00000074 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000075 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000076 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 OK 228872 47662.2 -2.26362 -1.16262 0.30655 0.380545 no +TCONS_00000077 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000078 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000079 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000080 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000081 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000082 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000083 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 OK 15591900 0 -inf - 0.12165 0.186975 no +TCONS_00000084 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 OK 294879 85971.3 -1.7782 -0.902752 0.36915 0.435206 no +TCONS_00000085 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 OK 807732 156995 -2.36316 -0.933704 0.4205 0.458727 no +TCONS_00000086 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000087 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000088 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000089 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000090 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 OK 7681690 0 -inf - 0.12165 0.186975 no +TCONS_00000091 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 OK 504790 0 -inf - 0.05945 0.186975 no +TCONS_00000092 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 OK 102717000 0 -inf - 0.12165 0.186975 no +TCONS_00000093 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 OK 3810010 0 -inf - 0.0148 0.101571 no +TCONS_00000094 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 OK 55365400 0 -inf - 0.0773 0.186975 no +TCONS_00000095 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 OK 62896600 0 -inf - 0.12165 0.186975 no +TCONS_00000096 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000097 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000098 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000099 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no +TCONS_00000100 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no diff -r 000000000000 -r 21d03c46f286 test-data/isoform_fpkm.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/isoform_fpkm.tabular Thu Apr 02 16:13:37 2015 -0400 @@ -0,0 +1,91 @@ +tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage q1_FPKM q1_conf_lo q1_conf_hi q1_status q2_FPKM q2_conf_lo q2_conf_hi q2_status +TCONS_00000001 c Xkr4 XLOC_000001 Xkr4 TCONS_00000001 chr1:3204754-3204833 79 - 0 0 0 OK 9459860 33303500 0 OK +TCONS_00000002 - - XLOC_000002 - TCONS_00000002 chr1:3111449-3111490 41 - 0 0 0 OK 243637000 952723000 0 OK +TCONS_00000003 - - XLOC_000003 - TCONS_00000003 chr1:3111545-3111576 31 - 0 0 0 OK 0 0 0 OK +TCONS_00000009 - - XLOC_000011 - TCONS_00000009 chr1:3192441-3192494 53 - 0 0 0 OK 97002000 317699000 0 OK +TCONS_00000010 - - XLOC_000012 - TCONS_00000010 chr1:3192550-3192629 79 - 0 0 0 OK 4729930 18496100 0 OK +TCONS_00000011 - - XLOC_000014 - TCONS_00000011 chr1:3192731-3192811 80 - 0 0 0 OK 0 0 0 OK +TCONS_00000012 - - XLOC_000015 - TCONS_00000012 chr1:3192940-3193042 102 - 0 0 0 OK 6863860 21424300 0 OK +TCONS_00000013 - - XLOC_000016 - TCONS_00000013 chr1:3194185-3194226 41 - 0 0 0 OK 243637000 952723000 0 OK +TCONS_00000014 - - XLOC_000017 - TCONS_00000014 chr1:3194302-3194329 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000015 - - XLOC_000019 - TCONS_00000015 chr1:3195083-3195110 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000016 - - XLOC_000020 - TCONS_00000016 chr1:3195450-3195477 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000017 - - XLOC_000021 - TCONS_00000017 chr1:3197089-3197116 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000018 - - XLOC_000022 - TCONS_00000018 chr1:3197246-3197273 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000019 - - XLOC_000023 - TCONS_00000019 chr1:3197346-3197373 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000020 - - XLOC_000025 - TCONS_00000020 chr1:3200022-3200191 169 - 826392 2653610 0 OK 803108 2630330 0 OK +TCONS_00000021 - - XLOC_000026 - TCONS_00000021 chr1:3200325-3200352 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000022 - - XLOC_000029 - TCONS_00000022 chr1:3201077-3201481 404 - 66791.3 214473 0 OK 324548 802006 0 OK +TCONS_00000023 - - XLOC_000031 - TCONS_00000023 chr1:3201672-3201699 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000024 i Xkr4 XLOC_000034 Xkr4 TCONS_00000024 chr1:3212213-3212292 79 - 0 0 0 OK 9459860 33303500 0 OK +TCONS_00000025 i Xkr4 XLOC_000035 Xkr4 TCONS_00000025 chr1:3212367-3212439 72 - 0 0 0 OK 28083700 87658400 0 OK +TCONS_00000026 i Xkr4 XLOC_000037 Xkr4 TCONS_00000026 chr1:3213095-3213242 97 - 4244630 15581400 0 OK 2082090 8141870 0 OK +TCONS_00000027 i Xkr4 XLOC_000040 Xkr4 TCONS_00000027 chr1:3242633-3242923 290 - 48522.7 185766 0 OK 424400 1302890 0 OK +TCONS_00000028 i Xkr4 XLOC_000042 Xkr4 TCONS_00000028 chr1:3243018-3243079 61 - 0 0 0 OK 30305300 106690000 0 OK +TCONS_00000029 i Xkr4 XLOC_000044 Xkr4 TCONS_00000029 chr1:3243347-3243401 54 - 0 0 0 OK 57999100 204186000 0 OK +TCONS_00000030 i Xkr4 XLOC_000046 Xkr4 TCONS_00000030 chr1:3256974-3257011 37 - 0 0 0 OK 2354230000 8288060000 0 OK +TCONS_00000031 i Xkr4 XLOC_000048 Xkr4 TCONS_00000031 chr1:3277190-3277218 28 - 0 0 0 OK 0 0 0 OK +TCONS_00000033 i Xkr4 XLOC_000052 Xkr4 TCONS_00000033 chr1:3280686-3280741 55 - 0 0 0 OK 26133400 102193000 0 OK +TCONS_00000034 i Xkr4 XLOC_000057 Xkr4 TCONS_00000034 chr1:3290488-3290553 65 - 0 0 0 OK 11150300 43602600 0 OK +TCONS_00000037 i Xkr4 XLOC_000060 Xkr4 TCONS_00000037 chr1:3299443-3299664 55 - 0 163195 0 OK 0 163195 0 OK +TCONS_00000038 i Xkr4 XLOC_000062 Xkr4 TCONS_00000038 chr1:3300051-3300078 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000039 i Xkr4 XLOC_000065 Xkr4 TCONS_00000039 chr1:3318999-3319051 52 - 0 0 0 OK 0 0 0 OK +TCONS_00000040 i Xkr4 XLOC_000068 Xkr4 TCONS_00000040 chr1:3355887-3356119 27 - 0 332434 0 OK 0 0 0 OK +TCONS_00000041 i Xkr4 XLOC_000071 Xkr4 TCONS_00000041 chr1:3363214-3363278 64 - 0 0 0 OK 0 0 0 OK +TCONS_00000042 i Xkr4 XLOC_000073 Xkr4 TCONS_00000042 chr1:3363753-3363849 96 - 0 0 0 OK 0 0 0 OK +TCONS_00000043 i Xkr4 XLOC_000075 Xkr4 TCONS_00000043 chr1:3367135-3367162 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000044 i Xkr4 XLOC_000077 Xkr4 TCONS_00000044 chr1:3367333-3367382 49 - 0 0 0 OK 0 0 0 OK +TCONS_00000045 i Xkr4 XLOC_000080 Xkr4 TCONS_00000045 chr1:3377211-3377262 51 - 0 0 0 OK 0 0 0 OK +TCONS_00000046 i Xkr4 XLOC_000083 Xkr4 TCONS_00000046 chr1:3391325-3391352 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000047 i Xkr4 XLOC_000084 Xkr4 TCONS_00000047 chr1:3435841-3435880 39 - 0 0 0 OK 0 0 0 OK +TCONS_00000048 i Xkr4 XLOC_000085 Xkr4 TCONS_00000048 chr1:3447761-3447788 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000049 i Xkr4 XLOC_000086 Xkr4 TCONS_00000049 chr1:3450906-3450965 59 - 0 0 0 OK 0 0 0 OK +TCONS_00000050 i Xkr4 XLOC_000087 Xkr4 TCONS_00000050 chr1:3451051-3451109 58 - 0 0 0 OK 0 0 0 OK +TCONS_00000051 - - XLOC_000004 - TCONS_00000051 chr1:3174765-3174792 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000052 - - XLOC_000005 - TCONS_00000052 chr1:3187401-3187428 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000053 - - XLOC_000006 - TCONS_00000053 chr1:3188521-3188548 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000054 - - XLOC_000007 - TCONS_00000054 chr1:3189810-3190789 979 - 358326 581565 135086 OK 522345 633911 410780 OK +TCONS_00000055 - - XLOC_000008 - TCONS_00000055 chr1:3190858-3191434 576 - 408511 762496 54526.1 OK 420354 779200 61509.1 OK +TCONS_00000056 - - XLOC_000009 - TCONS_00000056 chr1:3191512-3192077 565 - 433286 803020 63552.3 OK 842157 1341790 342520 OK +TCONS_00000057 - - XLOC_000010 - TCONS_00000057 chr1:3192250-3192336 86 - 3441510 13175600 0 OK 3344550 13078600 0 OK +TCONS_00000058 - - XLOC_000013 - TCONS_00000058 chr1:3192649-3192676 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000059 - - XLOC_000018 - TCONS_00000059 chr1:3194706-3194733 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000060 - - XLOC_000024 - TCONS_00000060 chr1:3197425-3197452 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000062 - - XLOC_000027 - TCONS_00000062 chr1:3200430-3200457 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000063 - - XLOC_000028 - TCONS_00000063 chr1:3201007-3201039 32 - 0 0 0 OK 0 0 0 OK +TCONS_00000065 - - XLOC_000030 - TCONS_00000065 chr1:3201596-3201666 70 - 16359000 59640900 0 OK 0 0 0 OK +TCONS_00000066 - - XLOC_000032 - TCONS_00000066 chr1:3201725-3201809 84 - 15136000 46339600 0 OK 0 0 0 OK +TCONS_00000067 i Xkr4 XLOC_000033 Xkr4 TCONS_00000067 chr1:3211521-3211561 40 - 0 0 0 OK 0 0 0 OK +TCONS_00000068 i Xkr4 XLOC_000036 Xkr4 TCONS_00000068 chr1:3212717-3212801 84 - 3784000 14486800 0 OK 0 0 0 OK +TCONS_00000069 i Xkr4 XLOC_000037 Xkr4 TCONS_00000069 chr1:3213095-3213242 124 - 863189 4252220 0 OK 0 72384.9 0 OK +TCONS_00000070 i Xkr4 XLOC_000038 Xkr4 TCONS_00000070 chr1:3240606-3240633 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000071 i Xkr4 XLOC_000039 Xkr4 TCONS_00000071 chr1:3242479-3242512 33 - 0 0 0 OK 0 0 0 OK +TCONS_00000072 i Xkr4 XLOC_000041 Xkr4 TCONS_00000072 chr1:3242924-3243005 81 - 0 0 0 OK 0 0 0 OK +TCONS_00000073 i Xkr4 XLOC_000043 Xkr4 TCONS_00000073 chr1:3243108-3243154 46 - 86160000 329857000 0 OK 0 0 0 OK +TCONS_00000074 i Xkr4 XLOC_000045 Xkr4 TCONS_00000074 chr1:3254079-3254106 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000075 i Xkr4 XLOC_000047 Xkr4 TCONS_00000075 chr1:3277155-3277182 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000076 i Xkr4 XLOC_000049 Xkr4 TCONS_00000076 chr1:3277913-3278390 477 - 228872 561229 0 OK 47662.2 156103 0 OK +TCONS_00000077 i Xkr4 XLOC_000050 Xkr4 TCONS_00000077 chr1:3280117-3280144 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000078 i Xkr4 XLOC_000051 Xkr4 TCONS_00000078 chr1:3280498-3280525 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000079 i Xkr4 XLOC_000053 Xkr4 TCONS_00000079 chr1:3282504-3282531 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000080 i Xkr4 XLOC_000054 Xkr4 TCONS_00000080 chr1:3282650-3282677 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000081 i Xkr4 XLOC_000055 Xkr4 TCONS_00000081 chr1:3282760-3282832 72 - 0 0 0 OK 0 0 0 OK +TCONS_00000082 i Xkr4 XLOC_000056 Xkr4 TCONS_00000082 chr1:3284966-3284993 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000083 i Xkr4 XLOC_000058 Xkr4 TCONS_00000083 chr1:3290798-3290859 61 - 15591900 59692600 0 OK 0 0 0 OK +TCONS_00000084 i Xkr4 XLOC_000059 Xkr4 TCONS_00000084 chr1:3290919-3291273 354 - 294879 740137 0 OK 85971.3 281572 0 OK +TCONS_00000085 i Xkr4 XLOC_000060 Xkr4 TCONS_00000085 chr1:3299443-3299664 197 - 807732 2390560 0 OK 156995 613917 0 OK +TCONS_00000086 i Xkr4 XLOC_000061 Xkr4 TCONS_00000086 chr1:3299691-3299733 42 - 0 0 0 OK 0 0 0 OK +TCONS_00000087 i Xkr4 XLOC_000063 Xkr4 TCONS_00000087 chr1:3307748-3307775 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000088 i Xkr4 XLOC_000064 Xkr4 TCONS_00000088 chr1:3318620-3318647 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000089 i Xkr4 XLOC_000066 Xkr4 TCONS_00000089 chr1:3330527-3330554 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000090 i Xkr4 XLOC_000067 Xkr4 TCONS_00000090 chr1:3351240-3351311 71 - 7681690 29408800 0 OK 0 0 0 OK +TCONS_00000091 i Xkr4 XLOC_000068 Xkr4 TCONS_00000091 chr1:3355887-3356119 212 - 504790 1545440 0 OK 0 0 0 OK +TCONS_00000092 i Xkr4 XLOC_000069 Xkr4 TCONS_00000092 chr1:3356180-3356225 45 - 102717000 393246000 0 OK 0 0 0 OK +TCONS_00000093 i Xkr4 XLOC_000070 Xkr4 TCONS_00000093 chr1:3363076-3363176 100 - 3810010 13890300 0 OK 0 0 0 OK +TCONS_00000094 i Xkr4 XLOC_000072 Xkr4 TCONS_00000094 chr1:3363387-3363446 59 - 55365400 177783000 0 OK 0 0 0 OK +TCONS_00000095 i Xkr4 XLOC_000074 Xkr4 TCONS_00000095 chr1:3364871-3364919 48 - 62896600 240795000 0 OK 0 0 0 OK +TCONS_00000096 i Xkr4 XLOC_000076 Xkr4 TCONS_00000096 chr1:3367210-3367237 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000097 i Xkr4 XLOC_000078 Xkr4 TCONS_00000097 chr1:3369580-3369607 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000098 i Xkr4 XLOC_000079 Xkr4 TCONS_00000098 chr1:3375001-3375028 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000099 i Xkr4 XLOC_000081 Xkr4 TCONS_00000099 chr1:3379888-3379915 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000100 i Xkr4 XLOC_000082 Xkr4 TCONS_00000100 chr1:3386739-3386836 97 - 0 0 0 OK 0 0 0 OK diff -r 000000000000 -r 21d03c46f286 test-data/isoform_rg.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/isoform_rg.tabular Thu Apr 02 16:13:37 2015 -0400 @@ -0,0 +1,181 @@ +tracking_id condition replicate raw_frags internal_scaled_frags external_scaled_frags FPKM effective_length status +TCONS_00000001 q1 0 0 0 0 0 - OK +TCONS_00000001 q2 0 2 1.94365 1.94365 9459860 - OK +TCONS_00000002 q1 0 0 0 0 0 - OK +TCONS_00000002 q2 0 1 0.971825 0.971825 243637000 - OK +TCONS_00000003 q1 0 0 0 0 0 - OK +TCONS_00000003 q2 0 0 0 0 0 - OK +TCONS_00000009 q1 0 0 0 0 0 - OK +TCONS_00000009 q2 0 3 2.91548 2.91548 97002000 - OK +TCONS_00000010 q1 0 0 0 0 0 - OK +TCONS_00000010 q2 0 1 0.971825 0.971825 4729930 - OK +TCONS_00000011 q1 0 0 0 0 0 - OK +TCONS_00000011 q2 0 0 0 0 0 - OK +TCONS_00000012 q1 0 0 0 0 0 - OK +TCONS_00000012 q2 0 4 3.8873 3.8873 6863860 - OK +TCONS_00000013 q1 0 0 0 0 0 - OK +TCONS_00000013 q2 0 1 0.971825 0.971825 243637000 - OK +TCONS_00000014 q1 0 0 0 0 0 - OK +TCONS_00000014 q2 0 0 0 0 0 - OK +TCONS_00000015 q1 0 0 0 0 0 - OK +TCONS_00000015 q2 0 0 0 0 0 - OK +TCONS_00000016 q1 0 0 0 0 0 - OK +TCONS_00000016 q2 0 0 0 0 0 - OK +TCONS_00000017 q1 0 0 0 0 0 - OK +TCONS_00000017 q2 0 0 0 0 0 - OK +TCONS_00000018 q1 0 0 0 0 0 - OK +TCONS_00000018 q2 0 0 0 0 0 - OK +TCONS_00000019 q1 0 0 0 0 0 - OK +TCONS_00000019 q2 0 0 0 0 0 - OK +TCONS_00000020 q1 0 3 3 3 826392 - OK +TCONS_00000020 q2 0 3 2.91548 2.91548 803108 - OK +TCONS_00000021 q1 0 0 0 0 0 - OK +TCONS_00000021 q2 0 0 0 0 0 - OK +TCONS_00000022 q1 0 3 3 3 66791.3 - OK +TCONS_00000022 q2 0 15 14.5774 14.5774 324548 - OK +TCONS_00000023 q1 0 0 0 0 0 - OK +TCONS_00000023 q2 0 0 0 0 0 - OK +TCONS_00000024 q1 0 0 0 0 0 - OK +TCONS_00000024 q2 0 2 1.94365 1.94365 9459860 - OK +TCONS_00000025 q1 0 0 0 0 0 - OK +TCONS_00000025 q2 0 4 3.8873 3.8873 28083700 - OK +TCONS_00000026 q1 0 1.9812 1.9812 1.9812 4244630 - OK +TCONS_00000026 q2 0 1 0.971825 0.971825 2082090 - OK +TCONS_00000027 q1 0 1 1 1 48522.7 - OK +TCONS_00000027 q2 0 9 8.74643 8.74643 424400 - OK +TCONS_00000028 q1 0 0 0 0 0 - OK +TCONS_00000028 q2 0 2 1.94365 1.94365 30305300 - OK +TCONS_00000029 q1 0 0 0 0 0 - OK +TCONS_00000029 q2 0 2 1.94365 1.94365 57999100 - OK +TCONS_00000030 q1 0 0 0 0 0 - OK +TCONS_00000030 q2 0 2 1.94365 1.94365 2354230000 - OK +TCONS_00000031 q1 0 0 0 0 0 - OK +TCONS_00000031 q2 0 0 0 0 0 - OK +TCONS_00000033 q1 0 0 0 0 0 - OK +TCONS_00000033 q2 0 1 0.971825 0.971825 26133400 - OK +TCONS_00000034 q1 0 0 0 0 0 - OK +TCONS_00000034 q2 0 1 0.971825 0.971825 11150300 - OK +TCONS_00000037 q1 0 0 0 0 0 - OK +TCONS_00000037 q2 0 0 0 0 0 - OK +TCONS_00000038 q1 0 0 0 0 0 - OK +TCONS_00000038 q2 0 0 0 0 0 - OK +TCONS_00000039 q1 0 0 0 0 0 - OK +TCONS_00000039 q2 0 0 0 0 0 - OK +TCONS_00000040 q1 0 0 0 0 0 - OK +TCONS_00000040 q2 0 0 0 0 0 - OK +TCONS_00000041 q1 0 0 0 0 0 - OK +TCONS_00000041 q2 0 0 0 0 0 - OK +TCONS_00000042 q1 0 0 0 0 0 - OK +TCONS_00000042 q2 0 0 0 0 0 - OK +TCONS_00000043 q1 0 0 0 0 0 - OK +TCONS_00000043 q2 0 0 0 0 0 - OK +TCONS_00000044 q1 0 0 0 0 0 - OK +TCONS_00000044 q2 0 0 0 0 0 - OK +TCONS_00000045 q1 0 0 0 0 0 - OK +TCONS_00000045 q2 0 0 0 0 0 - OK +TCONS_00000046 q1 0 0 0 0 0 - OK +TCONS_00000046 q2 0 0 0 0 0 - OK +TCONS_00000047 q1 0 0 0 0 0 - OK +TCONS_00000047 q2 0 0 0 0 0 - OK +TCONS_00000048 q1 0 0 0 0 0 - OK +TCONS_00000048 q2 0 0 0 0 0 - OK +TCONS_00000049 q1 0 0 0 0 0 - OK +TCONS_00000049 q2 0 0 0 0 0 - OK +TCONS_00000050 q1 0 0 0 0 0 - OK +TCONS_00000050 q2 0 0 0 0 0 - OK +TCONS_00000051 q1 0 0 0 0 0 - OK +TCONS_00000051 q2 0 0 0 0 0 - OK +TCONS_00000052 q1 0 0 0 0 0 - OK +TCONS_00000052 q2 0 0 0 0 0 - OK +TCONS_00000053 q1 0 0 0 0 0 - OK +TCONS_00000053 q2 0 0 0 0 0 - OK +TCONS_00000054 q1 0 62 62 62 358326 - OK +TCONS_00000054 q2 0 93 90.3798 90.3798 522345 - OK +TCONS_00000055 q1 0 34 34 34 408511 - OK +TCONS_00000055 q2 0 36 34.9857 34.9857 420354 - OK +TCONS_00000056 q1 0 35 35 35 433286 - OK +TCONS_00000056 q2 0 70 68.0278 68.0278 842157 - OK +TCONS_00000057 q1 0 1 1 1 3441510 - OK +TCONS_00000057 q2 0 1 0.971825 0.971825 3344550 - OK +TCONS_00000058 q1 0 0 0 0 0 - OK +TCONS_00000058 q2 0 0 0 0 0 - OK +TCONS_00000059 q1 0 0 0 0 0 - OK +TCONS_00000059 q2 0 0 0 0 0 - OK +TCONS_00000060 q1 0 0 0 0 0 - OK +TCONS_00000060 q2 0 0 0 0 0 - OK +TCONS_00000062 q1 0 0 0 0 0 - OK +TCONS_00000062 q2 0 0 0 0 0 - OK +TCONS_00000063 q1 0 0 0 0 0 - OK +TCONS_00000063 q2 0 0 0 0 0 - OK +TCONS_00000065 q1 0 2 2 2 16359000 - OK +TCONS_00000065 q2 0 0 0 0 0 - OK +TCONS_00000066 q1 0 4 4 4 15136000 - OK +TCONS_00000066 q2 0 0 0 0 0 - OK +TCONS_00000067 q1 0 0 0 0 0 - OK +TCONS_00000067 q2 0 0 0 0 0 - OK +TCONS_00000068 q1 0 1 1 1 3784000 - OK +TCONS_00000068 q2 0 0 0 0 0 - OK +TCONS_00000069 q1 0 1.0188 1.0188 1.0188 863189 - OK +TCONS_00000069 q2 0 0 0 0 0 - OK +TCONS_00000070 q1 0 0 0 0 0 - OK +TCONS_00000070 q2 0 0 0 0 0 - OK +TCONS_00000071 q1 0 0 0 0 0 - OK +TCONS_00000071 q2 0 0 0 0 0 - OK +TCONS_00000072 q1 0 0 0 0 0 - OK +TCONS_00000072 q2 0 0 0 0 0 - OK +TCONS_00000073 q1 0 1 1 1 86160000 - OK +TCONS_00000073 q2 0 0 0 0 0 - OK +TCONS_00000074 q1 0 0 0 0 0 - OK +TCONS_00000074 q2 0 0 0 0 0 - OK +TCONS_00000075 q1 0 0 0 0 0 - OK +TCONS_00000075 q2 0 0 0 0 0 - OK +TCONS_00000076 q1 0 14 14 14 228872 - OK +TCONS_00000076 q2 0 3 2.91548 2.91548 47662.2 - OK +TCONS_00000077 q1 0 0 0 0 0 - OK +TCONS_00000077 q2 0 0 0 0 0 - OK +TCONS_00000078 q1 0 0 0 0 0 - OK +TCONS_00000078 q2 0 0 0 0 0 - OK +TCONS_00000079 q1 0 0 0 0 0 - OK +TCONS_00000079 q2 0 0 0 0 0 - OK +TCONS_00000080 q1 0 0 0 0 0 - OK +TCONS_00000080 q2 0 0 0 0 0 - OK +TCONS_00000081 q1 0 0 0 0 0 - OK +TCONS_00000081 q2 0 0 0 0 0 - OK +TCONS_00000082 q1 0 0 0 0 0 - OK +TCONS_00000082 q2 0 0 0 0 0 - OK +TCONS_00000083 q1 0 1 1 1 15591900 - OK +TCONS_00000083 q2 0 0 0 0 0 - OK +TCONS_00000084 q1 0 10 10 10 294879 - OK +TCONS_00000084 q2 0 3 2.91548 2.91548 85971.3 - OK +TCONS_00000085 q1 0 5 5 5 807732 - OK +TCONS_00000085 q2 0 1 0.971825 0.971825 156995 - OK +TCONS_00000086 q1 0 0 0 0 0 - OK +TCONS_00000086 q2 0 0 0 0 0 - OK +TCONS_00000087 q1 0 0 0 0 0 - OK +TCONS_00000087 q2 0 0 0 0 0 - OK +TCONS_00000088 q1 0 0 0 0 0 - OK +TCONS_00000088 q2 0 0 0 0 0 - OK +TCONS_00000089 q1 0 0 0 0 0 - OK +TCONS_00000089 q2 0 0 0 0 0 - OK +TCONS_00000090 q1 0 1 1 1 7681690 - OK +TCONS_00000090 q2 0 0 0 0 0 - OK +TCONS_00000091 q1 0 4 4 4 504790 - OK +TCONS_00000091 q2 0 0 0 0 0 - OK +TCONS_00000092 q1 0 1 1 1 102717000 - OK +TCONS_00000092 q2 0 0 0 0 0 - OK +TCONS_00000093 q1 0 2 2 2 3810010 - OK +TCONS_00000093 q2 0 0 0 0 0 - OK +TCONS_00000094 q1 0 3 3 3 55365400 - OK +TCONS_00000094 q2 0 0 0 0 0 - OK +TCONS_00000095 q1 0 1 1 1 62896600 - OK +TCONS_00000095 q2 0 0 0 0 0 - OK +TCONS_00000096 q1 0 0 0 0 0 - OK +TCONS_00000096 q2 0 0 0 0 0 - OK +TCONS_00000097 q1 0 0 0 0 0 - OK +TCONS_00000097 q2 0 0 0 0 0 - OK +TCONS_00000098 q1 0 0 0 0 0 - OK +TCONS_00000098 q2 0 0 0 0 0 - OK +TCONS_00000099 q1 0 0 0 0 0 - OK +TCONS_00000099 q2 0 0 0 0 0 - OK +TCONS_00000100 q1 0 0 0 0 0 - OK +TCONS_00000100 q2 0 0 0 0 0 - OK diff -r 000000000000 -r 21d03c46f286 test-data/promoters_diff.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/promoters_diff.tabular Thu Apr 02 16:13:37 2015 -0400 @@ -0,0 +1,88 @@ +test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant +XLOC_000001 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000004 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000005 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000006 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000007 XLOC_000007 - chr1:3189810-3190789 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000008 XLOC_000008 - chr1:3190858-3191434 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000009 XLOC_000009 - chr1:3191512-3192077 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000010 XLOC_000010 - chr1:3192250-3192336 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000011 XLOC_000011 - chr1:3192441-3192494 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000012 XLOC_000012 - chr1:3192550-3192629 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000013 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000014 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000015 XLOC_000015 - chr1:3192940-3193042 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000016 XLOC_000016 - chr1:3194185-3194226 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000017 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000018 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000019 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000020 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000021 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000022 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000023 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000024 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000025 XLOC_000025 - chr1:3200022-3200191 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000026 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000027 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000028 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000029 XLOC_000029 - chr1:3201077-3201481 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000030 XLOC_000030 - chr1:3201596-3201666 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000031 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000032 XLOC_000032 - chr1:3201725-3201809 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000033 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000034 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000035 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000036 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000037 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000038 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000039 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000040 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000041 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000042 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000043 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000044 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000045 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000046 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000047 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000048 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000049 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000050 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000051 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000052 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000053 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000054 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000055 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000056 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000057 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000058 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000059 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000060 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000061 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000062 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000063 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000064 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000065 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000066 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000067 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000068 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000069 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000070 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000071 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000072 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000073 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000074 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000075 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000076 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000077 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000078 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000079 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000080 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000081 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000082 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000083 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000084 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000085 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000086 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000087 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no diff -r 000000000000 -r 21d03c46f286 test-data/read_groups.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/read_groups.tabular Thu Apr 02 16:13:37 2015 -0400 @@ -0,0 +1,3 @@ +file condition replicate_num total_mass norm_mass internal_scale external_scale +/tmp/tmpP3BAPq/tmpDkU5ls/database/files/000/dataset_26.dat q1 0 192 222.823 1 1 +/tmp/tmpP3BAPq/tmpDkU5ls/database/files/000/dataset_27.dat q2 0 261 222.823 1.02899 1 diff -r 000000000000 -r 21d03c46f286 test-data/run_info.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/run_info.tabular Thu Apr 02 16:13:37 2015 -0400 @@ -0,0 +1,5 @@ +param value +cmd_line cuffdiff --no-update-check --FDR=0.05 --num-threads=1 --min-alignment-count=0 --library-norm-method=geometric --dispersion-method=pooled --labels q1,q2 /tmp/tmpP3BAPq/tmpDkU5ls/database/files/000/dataset_25.dat /tmp/tmpP3BAPq/tmpDkU5ls/database/files/000/dataset_26.dat /tmp/tmpP3BAPq/tmpDkU5ls/database/files/000/dataset_27.dat +version 2.2.1 +SVN_revision 4237 +boost_version 104700 diff -r 000000000000 -r 21d03c46f286 test-data/splicing_diff.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/splicing_diff.tabular Thu Apr 02 16:13:37 2015 -0400 @@ -0,0 +1,89 @@ +test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant +TSS1 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS10 XLOC_000008 - chr1:3190858-3191434 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS11 XLOC_000009 - chr1:3191512-3192077 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS13 XLOC_000010 - chr1:3192250-3192336 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS14 XLOC_000011 - chr1:3192441-3192494 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS15 XLOC_000012 - chr1:3192550-3192629 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS16 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS17 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS18 XLOC_000015 - chr1:3192940-3193042 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS19 XLOC_000016 - chr1:3194185-3194226 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS2 XLOC_000002 - chr1:3111449-3111490 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS20 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS21 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS22 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS23 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS24 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS25 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS26 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS27 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS28 XLOC_000025 - chr1:3200022-3200191 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS29 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS3 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS30 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS31 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS32 XLOC_000029 - chr1:3201077-3201481 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS33 XLOC_000030 - chr1:3201596-3201666 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS34 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS35 XLOC_000032 - chr1:3201725-3201809 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS36 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS37 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS38 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS39 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS4 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS40 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 0 0 0.249947 0 0.5526 1 no +TSS41 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS42 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS43 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS44 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS45 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS46 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS47 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS48 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS49 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS5 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS50 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS51 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS52 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS54 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS55 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS56 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS57 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS58 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS59 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS6 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS60 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS61 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS62 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS63 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS65 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS66 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS67 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS68 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS69 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS7 XLOC_000007 - chr1:3189810-3190789 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS70 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS71 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS72 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS73 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS74 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS75 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS76 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS77 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS78 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS79 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS80 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS81 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS82 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS83 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS84 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS85 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS86 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS87 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS88 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS89 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS90 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS91 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS92 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS93 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no diff -r 000000000000 -r 21d03c46f286 test-data/tss_count_tracking.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tss_count_tracking.tabular Thu Apr 02 16:13:37 2015 -0400 @@ -0,0 +1,89 @@ +tracking_id q1_count q1_count_variance q1_count_uncertainty_var q1_count_dispersion_var q1_status q2_count q2_count_variance q2_count_uncertainty_var q2_count_dispersion_var q2_status +TSS1 0 0 0 0 OK 1.94365 6 0 5.96791 OK +TSS10 34 217 0 216.229 OK 34.9857 223 0 222.222 OK +TSS11 35 223 0 222.301 OK 68.0278 407.225 0 405.846 OK +TSS13 1 2 0 1.78395 OK 0.971825 2 0 1.66607 OK +TSS14 0 0 0 0 OK 2.91548 11 0 10.1281 OK +TSS15 0 0 0 0 OK 0.971825 2 0 1.66607 OK +TSS16 0 0 0 0 OK 0 0 0 0 OK +TSS17 0 0 0 0 OK 0 0 0 0 OK +TSS18 0 0 0 0 OK 3.8873 17 0 16.2636 OK +TSS19 0 0 0 0 OK 0.971825 2 0 1.66607 OK +TSS2 0 0 0 0 OK 0.971825 2 0 1.66607 OK +TSS20 0 0 0 0 OK 0 0 0 0 OK +TSS21 0 0 0 0 OK 0 0 0 0 OK +TSS22 0 0 0 0 OK 0 0 0 0 OK +TSS23 0 0 0 0 OK 0 0 0 0 OK +TSS24 0 0 0 0 OK 0 0 0 0 OK +TSS25 0 0 0 0 OK 0 0 0 0 OK +TSS26 0 0 0 0 OK 0 0 0 0 OK +TSS27 0 0 0 0 OK 0 0 0 0 OK +TSS28 3 11 0 10.5107 OK 2.91548 11 0 10.1281 OK +TSS29 0 0 0 0 OK 0 0 0 0 OK +TSS3 0 0 0 0 OK 0 0 0 0 OK +TSS30 0 0 0 0 OK 0 0 0 0 OK +TSS31 0 0 0 0 OK 0 0 0 0 OK +TSS32 3 11 0 10.5107 OK 14.5774 114.978 0 87.355 OK +TSS33 2 7 0 6.18584 OK 0 0 0 0 OK +TSS34 0 0 0 0 OK 0 0 0 0 OK +TSS35 4 17 0 16.9943 OK 0 0 0 0 OK +TSS36 0 0 0 0 OK 0 0 0 0 OK +TSS37 0 0 0 0 OK 1.94365 6 0 5.96791 OK +TSS38 0 0 0 0 OK 3.8873 17 0 16.2636 OK +TSS39 1 2 0 1.78395 OK 0 0 0 0 OK +TSS4 0 0 0 0 OK 0 0 0 0 OK +TSS40 3 11.0603 0 10.5107 OK 0.971825 2.99194 0 1.66607 OK +TSS41 0 0 0 0 OK 0 0 0 0 OK +TSS42 0 0 0 0 OK 0 0 0 0 OK +TSS43 1 2 0 1.78395 OK 8.74643 81.9454 0 48.6822 OK +TSS44 0 0 0 0 OK 0 0 0 0 OK +TSS45 0 0 0 0 OK 1.94365 6 0 5.96791 OK +TSS46 1 2 0 1.78395 OK 0 0 0 0 OK +TSS47 0 0 0 0 OK 1.94365 6 0 5.96791 OK +TSS48 0 0 0 0 OK 0 0 0 0 OK +TSS49 0 0 0 0 OK 1.94365 6 0 5.96791 OK +TSS5 0 0 0 0 OK 0 0 0 0 OK +TSS50 0 0 0 0 OK 0 0 0 0 OK +TSS51 0 0 0 0 OK 0 0 0 0 OK +TSS52 14 103.329 0 83.524 OK 2.91548 11 0 10.1281 OK +TSS54 0 0 0 0 OK 0 0 0 0 OK +TSS55 0 0 0 0 OK 0 0 0 0 OK +TSS56 0 0 0 0 OK 0.971825 2 0 1.66607 OK +TSS57 0 0 0 0 OK 0 0 0 0 OK +TSS58 0 0 0 0 OK 0 0 0 0 OK +TSS59 0 0 0 0 OK 0 0 0 0 OK +TSS6 0 0 0 0 OK 0 0 0 0 OK +TSS60 0 0 0 0 OK 0 0 0 0 OK +TSS61 0 0 0 0 OK 0.971825 2 0 1.66607 OK +TSS62 1 2 0 1.78395 OK 0 0 0 0 OK +TSS63 10 57 0 56.983 OK 2.91548 11 0 10.1281 OK +TSS65 5 24 0 23.5132 OK 0.971825 2 0 1.66607 OK +TSS66 0 1 0 0 OK 0 1 0 0 OK +TSS67 0 0 0 0 OK 0 0 0 0 OK +TSS68 0 0 0 0 OK 0 0 0 0 OK +TSS69 0 0 0 0 OK 0 0 0 0 OK +TSS7 62 373 0 372.146 OK 90.3798 93.159 0 90.3798 OK +TSS70 0 0 0 0 OK 0 0 0 0 OK +TSS71 0 0 0 0 OK 0 0 0 0 OK +TSS72 0 0 0 0 OK 0 0 0 0 OK +TSS73 1 2 0 1.78395 OK 0 0 0 0 OK +TSS74 4 17.9966 0 16.9943 OK 0 0 0 0 OK +TSS75 1 2 0 1.78395 OK 0 0 0 0 OK +TSS76 2 7 0 6.18584 OK 0 0 0 0 OK +TSS77 0 0 0 0 OK 0 0 0 0 OK +TSS78 3 11 0 10.5107 OK 0 0 0 0 OK +TSS79 0 0 0 0 OK 0 0 0 0 OK +TSS80 1 2 0 1.78395 OK 0 0 0 0 OK +TSS81 0 0 0 0 OK 0 0 0 0 OK +TSS82 0 0 0 0 OK 0 0 0 0 OK +TSS83 0 0 0 0 OK 0 0 0 0 OK +TSS84 0 0 0 0 OK 0 0 0 0 OK +TSS85 0 0 0 0 OK 0 0 0 0 OK +TSS86 0 0 0 0 OK 0 0 0 0 OK +TSS87 0 0 0 0 OK 0 0 0 0 OK +TSS88 0 0 0 0 OK 0 0 0 0 OK +TSS89 0 0 0 0 OK 0 0 0 0 OK +TSS90 0 0 0 0 OK 0 0 0 0 OK +TSS91 0 0 0 0 OK 0 0 0 0 OK +TSS92 0 0 0 0 OK 0 0 0 0 OK +TSS93 0 0 0 0 OK 0 0 0 0 OK diff -r 000000000000 -r 21d03c46f286 test-data/tss_fpkm.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tss_fpkm.tabular Thu Apr 02 16:13:37 2015 -0400 @@ -0,0 +1,89 @@ +tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage q1_FPKM q1_conf_lo q1_conf_hi q1_status q2_FPKM q2_conf_lo q2_conf_hi q2_status +TSS1 - - XLOC_000001 Xkr4 TSS1 chr1:3204754-3204833 - - 0 0 0 OK 9459860 33303500 0 OK +TSS10 - - XLOC_000008 - TSS10 chr1:3190858-3191434 - - 408511 762496 54526.1 OK 420354 779200 61509.1 OK +TSS11 - - XLOC_000009 - TSS11 chr1:3191512-3192077 - - 433286 803020 63552.3 OK 842157 1341790 342520 OK +TSS13 - - XLOC_000010 - TSS13 chr1:3192250-3192336 - - 3441510 13175600 0 OK 3344550 13078600 0 OK +TSS14 - - XLOC_000011 - TSS14 chr1:3192441-3192494 - - 0 0 0 OK 97002000 317699000 0 OK +TSS15 - - XLOC_000012 - TSS15 chr1:3192550-3192629 - - 0 0 0 OK 4729930 18496100 0 OK +TSS16 - - XLOC_000013 - TSS16 chr1:3192649-3192676 - - 0 0 0 OK 0 0 0 OK +TSS17 - - XLOC_000014 - TSS17 chr1:3192731-3192811 - - 0 0 0 OK 0 0 0 OK +TSS18 - - XLOC_000015 - TSS18 chr1:3192940-3193042 - - 0 0 0 OK 6863860 21424300 0 OK +TSS19 - - XLOC_000016 - TSS19 chr1:3194185-3194226 - - 0 0 0 OK 243637000 952723000 0 OK +TSS2 - - XLOC_000002 - TSS2 chr1:3111449-3111490 - - 0 0 0 OK 243637000 952723000 0 OK +TSS20 - - XLOC_000017 - TSS20 chr1:3194302-3194329 - - 0 0 0 OK 0 0 0 OK +TSS21 - - XLOC_000018 - TSS21 chr1:3194706-3194733 - - 0 0 0 OK 0 0 0 OK +TSS22 - - XLOC_000019 - TSS22 chr1:3195083-3195110 - - 0 0 0 OK 0 0 0 OK +TSS23 - - XLOC_000020 - TSS23 chr1:3195450-3195477 - - 0 0 0 OK 0 0 0 OK +TSS24 - - XLOC_000021 - TSS24 chr1:3197089-3197116 - - 0 0 0 OK 0 0 0 OK +TSS25 - - XLOC_000022 - TSS25 chr1:3197246-3197273 - - 0 0 0 OK 0 0 0 OK +TSS26 - - XLOC_000023 - TSS26 chr1:3197346-3197373 - - 0 0 0 OK 0 0 0 OK +TSS27 - - XLOC_000024 - TSS27 chr1:3197425-3197452 - - 0 0 0 OK 0 0 0 OK +TSS28 - - XLOC_000025 - TSS28 chr1:3200022-3200191 - - 826392 2653610 0 OK 803108 2630330 0 OK +TSS29 - - XLOC_000026 - TSS29 chr1:3200325-3200352 - - 0 0 0 OK 0 0 0 OK +TSS3 - - XLOC_000003 - TSS3 chr1:3111545-3111576 - - 0 0 0 OK 0 0 0 OK +TSS30 - - XLOC_000027 - TSS30 chr1:3200430-3200457 - - 0 0 0 OK 0 0 0 OK +TSS31 - - XLOC_000028 - TSS31 chr1:3201007-3201039 - - 0 0 0 OK 0 0 0 OK +TSS32 - - XLOC_000029 - TSS32 chr1:3201077-3201481 - - 66791.3 214473 0 OK 324548 802006 0 OK +TSS33 - - XLOC_000030 - TSS33 chr1:3201596-3201666 - - 16359000 59640900 0 OK 0 0 0 OK +TSS34 - - XLOC_000031 - TSS34 chr1:3201672-3201699 - - 0 0 0 OK 0 0 0 OK +TSS35 - - XLOC_000032 - TSS35 chr1:3201725-3201809 - - 15136000 46339600 0 OK 0 0 0 OK +TSS36 - - XLOC_000033 Xkr4 TSS36 chr1:3211521-3211561 - - 0 0 0 OK 0 0 0 OK +TSS37 - - XLOC_000034 Xkr4 TSS37 chr1:3212213-3212292 - - 0 0 0 OK 9459860 33303500 0 OK +TSS38 - - XLOC_000035 Xkr4 TSS38 chr1:3212367-3212439 - - 0 0 0 OK 28083700 87658400 0 OK +TSS39 - - XLOC_000036 Xkr4 TSS39 chr1:3212717-3212801 - - 3784000 14486800 0 OK 0 0 0 OK +TSS4 - - XLOC_000004 - TSS4 chr1:3174765-3174792 - - 0 0 0 OK 0 0 0 OK +TSS40 - - XLOC_000037 Xkr4 TSS40 chr1:3213095-3213242 - - 5107810 16958800 0 OK 2082090 8142100 0 OK +TSS41 - - XLOC_000038 Xkr4 TSS41 chr1:3240606-3240633 - - 0 0 0 OK 0 0 0 OK +TSS42 - - XLOC_000039 Xkr4 TSS42 chr1:3242479-3242512 - - 0 0 0 OK 0 0 0 OK +TSS43 - - XLOC_000040 Xkr4 TSS43 chr1:3242633-3242923 - - 48522.7 185766 0 OK 424400 1302890 0 OK +TSS44 - - XLOC_000041 Xkr4 TSS44 chr1:3242924-3243005 - - 0 0 0 OK 0 0 0 OK +TSS45 - - XLOC_000042 Xkr4 TSS45 chr1:3243018-3243079 - - 0 0 0 OK 30305300 106690000 0 OK +TSS46 - - XLOC_000043 Xkr4 TSS46 chr1:3243108-3243154 - - 86160000 329857000 0 OK 0 0 0 OK +TSS47 - - XLOC_000044 Xkr4 TSS47 chr1:3243347-3243401 - - 0 0 0 OK 57999100 204186000 0 OK +TSS48 - - XLOC_000045 Xkr4 TSS48 chr1:3254079-3254106 - - 0 0 0 OK 0 0 0 OK +TSS49 - - XLOC_000046 Xkr4 TSS49 chr1:3256974-3257011 - - 0 0 0 OK 2354230000 8288060000 0 OK +TSS5 - - XLOC_000005 - TSS5 chr1:3187401-3187428 - - 0 0 0 OK 0 0 0 OK +TSS50 - - XLOC_000047 Xkr4 TSS50 chr1:3277155-3277182 - - 0 0 0 OK 0 0 0 OK +TSS51 - - XLOC_000048 Xkr4 TSS51 chr1:3277190-3277218 - - 0 0 0 OK 0 0 0 OK +TSS52 - - XLOC_000049 Xkr4 TSS52 chr1:3277913-3278390 - - 228872 561229 0 OK 47662.2 156103 0 OK +TSS54 - - XLOC_000050 Xkr4 TSS54 chr1:3280117-3280144 - - 0 0 0 OK 0 0 0 OK +TSS55 - - XLOC_000051 Xkr4 TSS55 chr1:3280498-3280525 - - 0 0 0 OK 0 0 0 OK +TSS56 - - XLOC_000052 Xkr4 TSS56 chr1:3280686-3280741 - - 0 0 0 OK 26133400 102193000 0 OK +TSS57 - - XLOC_000053 Xkr4 TSS57 chr1:3282504-3282531 - - 0 0 0 OK 0 0 0 OK +TSS58 - - XLOC_000054 Xkr4 TSS58 chr1:3282650-3282677 - - 0 0 0 OK 0 0 0 OK +TSS59 - - XLOC_000055 Xkr4 TSS59 chr1:3282760-3282832 - - 0 0 0 OK 0 0 0 OK +TSS6 - - XLOC_000006 - TSS6 chr1:3188521-3188548 - - 0 0 0 OK 0 0 0 OK +TSS60 - - XLOC_000056 Xkr4 TSS60 chr1:3284966-3284993 - - 0 0 0 OK 0 0 0 OK +TSS61 - - XLOC_000057 Xkr4 TSS61 chr1:3290488-3290553 - - 0 0 0 OK 11150300 43602600 0 OK +TSS62 - - XLOC_000058 Xkr4 TSS62 chr1:3290798-3290859 - - 15591900 59692600 0 OK 0 0 0 OK +TSS63 - - XLOC_000059 Xkr4 TSS63 chr1:3290919-3291273 - - 294879 740137 0 OK 85971.3 281572 0 OK +TSS65 - - XLOC_000060 Xkr4 TSS65 chr1:3299443-3299664 - - 807732 2390560 0 OK 156995 613917 0 OK +TSS66 - - XLOC_000060 Xkr4 TSS66 chr1:3299443-3299664 - - 0 0 0 OK 0 0 0 OK +TSS67 - - XLOC_000061 Xkr4 TSS67 chr1:3299691-3299733 - - 0 0 0 OK 0 0 0 OK +TSS68 - - XLOC_000062 Xkr4 TSS68 chr1:3300051-3300078 - - 0 0 0 OK 0 0 0 OK +TSS69 - - XLOC_000063 Xkr4 TSS69 chr1:3307748-3307775 - - 0 0 0 OK 0 0 0 OK +TSS7 - - XLOC_000007 - TSS7 chr1:3189810-3190789 - - 358326 581565 135086 OK 522345 633911 410780 OK +TSS70 - - XLOC_000064 Xkr4 TSS70 chr1:3318620-3318647 - - 0 0 0 OK 0 0 0 OK +TSS71 - - XLOC_000065 Xkr4 TSS71 chr1:3318999-3319051 - - 0 0 0 OK 0 0 0 OK +TSS72 - - XLOC_000066 Xkr4 TSS72 chr1:3330527-3330554 - - 0 0 0 OK 0 0 0 OK +TSS73 - - XLOC_000067 Xkr4 TSS73 chr1:3351240-3351311 - - 7681690 29408800 0 OK 0 0 0 OK +TSS74 - - XLOC_000068 Xkr4 TSS74 chr1:3355887-3356119 - - 504790 1597120 0 OK 0 0 0 OK +TSS75 - - XLOC_000069 Xkr4 TSS75 chr1:3356180-3356225 - - 102717000 393246000 0 OK 0 0 0 OK +TSS76 - - XLOC_000070 Xkr4 TSS76 chr1:3363076-3363176 - - 3810010 13890300 0 OK 0 0 0 OK +TSS77 - - XLOC_000071 Xkr4 TSS77 chr1:3363214-3363278 - - 0 0 0 OK 0 0 0 OK +TSS78 - - XLOC_000072 Xkr4 TSS78 chr1:3363387-3363446 - - 55365400 177783000 0 OK 0 0 0 OK +TSS79 - - XLOC_000073 Xkr4 TSS79 chr1:3363753-3363849 - - 0 0 0 OK 0 0 0 OK +TSS80 - - XLOC_000074 Xkr4 TSS80 chr1:3364871-3364919 - - 62896600 240795000 0 OK 0 0 0 OK +TSS81 - - XLOC_000075 Xkr4 TSS81 chr1:3367135-3367162 - - 0 0 0 OK 0 0 0 OK +TSS82 - - XLOC_000076 Xkr4 TSS82 chr1:3367210-3367237 - - 0 0 0 OK 0 0 0 OK +TSS83 - - XLOC_000077 Xkr4 TSS83 chr1:3367333-3367382 - - 0 0 0 OK 0 0 0 OK +TSS84 - - XLOC_000078 Xkr4 TSS84 chr1:3369580-3369607 - - 0 0 0 OK 0 0 0 OK +TSS85 - - XLOC_000079 Xkr4 TSS85 chr1:3375001-3375028 - - 0 0 0 OK 0 0 0 OK +TSS86 - - XLOC_000080 Xkr4 TSS86 chr1:3377211-3377262 - - 0 0 0 OK 0 0 0 OK +TSS87 - - XLOC_000081 Xkr4 TSS87 chr1:3379888-3379915 - - 0 0 0 OK 0 0 0 OK +TSS88 - - XLOC_000082 Xkr4 TSS88 chr1:3386739-3386836 - - 0 0 0 OK 0 0 0 OK +TSS89 - - XLOC_000083 Xkr4 TSS89 chr1:3391325-3391352 - - 0 0 0 OK 0 0 0 OK +TSS90 - - XLOC_000084 Xkr4 TSS90 chr1:3435841-3435880 - - 0 0 0 OK 0 0 0 OK +TSS91 - - XLOC_000085 Xkr4 TSS91 chr1:3447761-3447788 - - 0 0 0 OK 0 0 0 OK +TSS92 - - XLOC_000086 Xkr4 TSS92 chr1:3450906-3450965 - - 0 0 0 OK 0 0 0 OK +TSS93 - - XLOC_000087 Xkr4 TSS93 chr1:3451051-3451109 - - 0 0 0 OK 0 0 0 OK diff -r 000000000000 -r 21d03c46f286 test-data/tss_group_exp.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tss_group_exp.tabular Thu Apr 02 16:13:37 2015 -0400 @@ -0,0 +1,89 @@ +test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant +TSS1 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 OK 0 9459860 inf - 0.01975 0.09875 no +TSS10 XLOC_000008 - chr1:3190858-3191434 q1 q2 OK 408511 420354 0.0412311 0.0469899 0.96715 0.96715 no +TSS11 XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 433286 842157 0.958769 1.27887 0.20385 0.274413 no +TSS13 XLOC_000010 - chr1:3192250-3192336 q1 q2 OK 3441510 3344550 -0.0412311 -0.014084 0.67715 0.718189 no +TSS14 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 97002000 inf - 0.07975 0.181781 no +TSS15 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 4729930 inf - 0.12465 0.181781 no +TSS16 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS17 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS18 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 6863860 inf - 0.0612 0.181781 no +TSS19 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 243637000 inf - 0.12465 0.181781 no +TSS2 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 243637000 inf - 0.12465 0.181781 no +TSS20 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS21 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS22 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS23 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS24 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS25 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS26 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS27 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS28 XLOC_000025 - chr1:3200022-3200191 q1 q2 OK 826392 803108 -0.0412311 -0.0180163 0.8625 0.887868 no +TSS29 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS3 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS30 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS31 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS32 XLOC_000029 - chr1:3201077-3201481 q1 q2 OK 66791.3 324548 2.2807 1.1905 0.3026 0.383188 no +TSS33 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 16359000 0 -inf - 0.0148 0.09875 no +TSS34 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS35 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 15136000 0 -inf - 0.06005 0.181781 no +TSS36 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS37 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 OK 0 9459860 inf - 0.01975 0.09875 no +TSS38 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 OK 0 28083700 inf - 0.0612 0.181781 no +TSS39 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 OK 3784000 0 -inf - 0.12165 0.181781 no +TSS4 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS40 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 OK 5107810 2082090 -1.29467 -0.482193 0.5916 0.647062 no +TSS41 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS42 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS43 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 OK 48522.7 424400 3.12869 1.23747 0.38685 0.451325 no +TSS44 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS45 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 OK 0 30305300 inf - 0.01975 0.09875 no +TSS46 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 OK 86160000 0 -inf - 0.12165 0.181781 no +TSS47 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 OK 0 57999100 inf - 0.01975 0.09875 no +TSS48 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS49 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 OK 0 2354230000 inf - 0.01975 0.09875 no +TSS5 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS50 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS51 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS52 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 OK 228872 47662.2 -2.26362 -1.16262 0.30655 0.383188 no +TSS54 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS55 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS56 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 OK 0 26133400 inf - 0.12465 0.181781 no +TSS57 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS58 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS59 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS6 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS60 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS61 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 OK 0 11150300 inf - 0.12465 0.181781 no +TSS62 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 OK 15591900 0 -inf - 0.12165 0.181781 no +TSS63 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 OK 294879 85971.3 -1.7782 -0.902752 0.36915 0.445526 no +TSS65 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 OK 807732 156995 -2.36316 -0.933704 0.4205 0.474758 no +TSS66 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS67 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS68 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS69 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS7 XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 358326 522345 0.543731 1.1445 0.1952 0.27328 no +TSS70 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS71 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS72 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS73 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 OK 7681690 0 -inf - 0.12165 0.181781 no +TSS74 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 OK 504790 0 -inf - 0.04565 0.181781 no +TSS75 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 OK 102717000 0 -inf - 0.12165 0.181781 no +TSS76 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 OK 3810010 0 -inf - 0.0148 0.09875 no +TSS77 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS78 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 OK 55365400 0 -inf - 0.0773 0.181781 no +TSS79 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS80 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 OK 62896600 0 -inf - 0.12165 0.181781 no +TSS81 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS82 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS83 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS84 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS85 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS86 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS87 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS88 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS89 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS90 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS91 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS92 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS93 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no diff -r 000000000000 -r 21d03c46f286 test-data/tss_rg.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tss_rg.tabular Thu Apr 02 16:13:37 2015 -0400 @@ -0,0 +1,177 @@ +tracking_id condition replicate raw_frags internal_scaled_frags external_scaled_frags FPKM effective_length status +TSS1 q1 0 0 0 0 0 - OK +TSS1 q2 0 2 1.94365 1.94365 9459860 - OK +TSS10 q1 0 34 34 34 408511 - OK +TSS10 q2 0 36 34.9857 34.9857 420354 - OK +TSS11 q1 0 35 35 35 433286 - OK +TSS11 q2 0 70 68.0278 68.0278 842157 - OK +TSS13 q1 0 1 1 1 3441510 - OK +TSS13 q2 0 1 0.971825 0.971825 3344550 - OK +TSS14 q1 0 0 0 0 0 - OK +TSS14 q2 0 3 2.91548 2.91548 97002000 - OK +TSS15 q1 0 0 0 0 0 - OK +TSS15 q2 0 1 0.971825 0.971825 4729930 - OK +TSS16 q1 0 0 0 0 0 - OK +TSS16 q2 0 0 0 0 0 - OK +TSS17 q1 0 0 0 0 0 - OK +TSS17 q2 0 0 0 0 0 - OK +TSS18 q1 0 0 0 0 0 - OK +TSS18 q2 0 4 3.8873 3.8873 6863860 - OK +TSS19 q1 0 0 0 0 0 - OK +TSS19 q2 0 1 0.971825 0.971825 243637000 - OK +TSS2 q1 0 0 0 0 0 - OK +TSS2 q2 0 1 0.971825 0.971825 243637000 - OK +TSS20 q1 0 0 0 0 0 - OK +TSS20 q2 0 0 0 0 0 - OK +TSS21 q1 0 0 0 0 0 - OK +TSS21 q2 0 0 0 0 0 - OK +TSS22 q1 0 0 0 0 0 - OK +TSS22 q2 0 0 0 0 0 - OK +TSS23 q1 0 0 0 0 0 - OK +TSS23 q2 0 0 0 0 0 - OK +TSS24 q1 0 0 0 0 0 - OK +TSS24 q2 0 0 0 0 0 - OK +TSS25 q1 0 0 0 0 0 - OK +TSS25 q2 0 0 0 0 0 - OK +TSS26 q1 0 0 0 0 0 - OK +TSS26 q2 0 0 0 0 0 - OK +TSS27 q1 0 0 0 0 0 - OK +TSS27 q2 0 0 0 0 0 - OK +TSS28 q1 0 3 3 3 826392 - OK +TSS28 q2 0 3 2.91548 2.91548 803108 - OK +TSS29 q1 0 0 0 0 0 - OK +TSS29 q2 0 0 0 0 0 - OK +TSS3 q1 0 0 0 0 0 - OK +TSS3 q2 0 0 0 0 0 - OK +TSS30 q1 0 0 0 0 0 - OK +TSS30 q2 0 0 0 0 0 - OK +TSS31 q1 0 0 0 0 0 - OK +TSS31 q2 0 0 0 0 0 - OK +TSS32 q1 0 3 3 3 66791.3 - OK +TSS32 q2 0 15 14.5774 14.5774 324548 - OK +TSS33 q1 0 2 2 2 16359000 - OK +TSS33 q2 0 0 0 0 0 - OK +TSS34 q1 0 0 0 0 0 - OK +TSS34 q2 0 0 0 0 0 - OK +TSS35 q1 0 4 4 4 15136000 - OK +TSS35 q2 0 0 0 0 0 - OK +TSS36 q1 0 0 0 0 0 - OK +TSS36 q2 0 0 0 0 0 - OK +TSS37 q1 0 0 0 0 0 - OK +TSS37 q2 0 2 1.94365 1.94365 9459860 - OK +TSS38 q1 0 0 0 0 0 - OK +TSS38 q2 0 4 3.8873 3.8873 28083700 - OK +TSS39 q1 0 1 1 1 3784000 - OK +TSS39 q2 0 0 0 0 0 - OK +TSS4 q1 0 0 0 0 0 - OK +TSS4 q2 0 0 0 0 0 - OK +TSS40 q1 0 3 3 3 5107810 - OK +TSS40 q2 0 1 0.971825 0.971825 2082090 - OK +TSS41 q1 0 0 0 0 0 - OK +TSS41 q2 0 0 0 0 0 - OK +TSS42 q1 0 0 0 0 0 - OK +TSS42 q2 0 0 0 0 0 - OK +TSS43 q1 0 1 1 1 48522.7 - OK +TSS43 q2 0 9 8.74643 8.74643 424400 - OK +TSS44 q1 0 0 0 0 0 - OK +TSS44 q2 0 0 0 0 0 - OK +TSS45 q1 0 0 0 0 0 - OK +TSS45 q2 0 2 1.94365 1.94365 30305300 - OK +TSS46 q1 0 1 1 1 86160000 - OK +TSS46 q2 0 0 0 0 0 - OK +TSS47 q1 0 0 0 0 0 - OK +TSS47 q2 0 2 1.94365 1.94365 57999100 - OK +TSS48 q1 0 0 0 0 0 - OK +TSS48 q2 0 0 0 0 0 - OK +TSS49 q1 0 0 0 0 0 - OK +TSS49 q2 0 2 1.94365 1.94365 2354230000 - OK +TSS5 q1 0 0 0 0 0 - OK +TSS5 q2 0 0 0 0 0 - OK +TSS50 q1 0 0 0 0 0 - OK +TSS50 q2 0 0 0 0 0 - OK +TSS51 q1 0 0 0 0 0 - OK +TSS51 q2 0 0 0 0 0 - OK +TSS52 q1 0 14 14 14 228872 - OK +TSS52 q2 0 3 2.91548 2.91548 47662.2 - OK +TSS54 q1 0 0 0 0 0 - OK +TSS54 q2 0 0 0 0 0 - OK +TSS55 q1 0 0 0 0 0 - OK +TSS55 q2 0 0 0 0 0 - OK +TSS56 q1 0 0 0 0 0 - OK +TSS56 q2 0 1 0.971825 0.971825 26133400 - OK +TSS57 q1 0 0 0 0 0 - OK +TSS57 q2 0 0 0 0 0 - OK +TSS58 q1 0 0 0 0 0 - OK +TSS58 q2 0 0 0 0 0 - OK +TSS59 q1 0 0 0 0 0 - OK +TSS59 q2 0 0 0 0 0 - OK +TSS6 q1 0 0 0 0 0 - OK +TSS6 q2 0 0 0 0 0 - OK +TSS60 q1 0 0 0 0 0 - OK +TSS60 q2 0 0 0 0 0 - OK +TSS61 q1 0 0 0 0 0 - OK +TSS61 q2 0 1 0.971825 0.971825 11150300 - OK +TSS62 q1 0 1 1 1 15591900 - OK +TSS62 q2 0 0 0 0 0 - OK +TSS63 q1 0 10 10 10 294879 - OK +TSS63 q2 0 3 2.91548 2.91548 85971.3 - OK +TSS65 q1 0 5 5 5 807732 - OK +TSS65 q2 0 1 0.971825 0.971825 156995 - OK +TSS66 q1 0 0 0 0 0 - OK +TSS66 q2 0 0 0 0 0 - OK +TSS67 q1 0 0 0 0 0 - OK +TSS67 q2 0 0 0 0 0 - OK +TSS68 q1 0 0 0 0 0 - OK +TSS68 q2 0 0 0 0 0 - OK +TSS69 q1 0 0 0 0 0 - OK +TSS69 q2 0 0 0 0 0 - OK +TSS7 q1 0 62 62 62 358326 - OK +TSS7 q2 0 93 90.3798 90.3798 522345 - OK +TSS70 q1 0 0 0 0 0 - OK +TSS70 q2 0 0 0 0 0 - OK +TSS71 q1 0 0 0 0 0 - OK +TSS71 q2 0 0 0 0 0 - OK +TSS72 q1 0 0 0 0 0 - OK +TSS72 q2 0 0 0 0 0 - OK +TSS73 q1 0 1 1 1 7681690 - OK +TSS73 q2 0 0 0 0 0 - OK +TSS74 q1 0 4 4 4 504790 - OK +TSS74 q2 0 0 0 0 0 - OK +TSS75 q1 0 1 1 1 102717000 - OK +TSS75 q2 0 0 0 0 0 - OK +TSS76 q1 0 2 2 2 3810010 - OK +TSS76 q2 0 0 0 0 0 - OK +TSS77 q1 0 0 0 0 0 - OK +TSS77 q2 0 0 0 0 0 - OK +TSS78 q1 0 3 3 3 55365400 - OK +TSS78 q2 0 0 0 0 0 - OK +TSS79 q1 0 0 0 0 0 - OK +TSS79 q2 0 0 0 0 0 - OK +TSS80 q1 0 1 1 1 62896600 - OK +TSS80 q2 0 0 0 0 0 - OK +TSS81 q1 0 0 0 0 0 - OK +TSS81 q2 0 0 0 0 0 - OK +TSS82 q1 0 0 0 0 0 - OK +TSS82 q2 0 0 0 0 0 - OK +TSS83 q1 0 0 0 0 0 - OK +TSS83 q2 0 0 0 0 0 - OK +TSS84 q1 0 0 0 0 0 - OK +TSS84 q2 0 0 0 0 0 - OK +TSS85 q1 0 0 0 0 0 - OK +TSS85 q2 0 0 0 0 0 - OK +TSS86 q1 0 0 0 0 0 - OK +TSS86 q2 0 0 0 0 0 - OK +TSS87 q1 0 0 0 0 0 - OK +TSS87 q2 0 0 0 0 0 - OK +TSS88 q1 0 0 0 0 0 - OK +TSS88 q2 0 0 0 0 0 - OK +TSS89 q1 0 0 0 0 0 - OK +TSS89 q2 0 0 0 0 0 - OK +TSS90 q1 0 0 0 0 0 - OK +TSS90 q2 0 0 0 0 0 - OK +TSS91 q1 0 0 0 0 0 - OK +TSS91 q2 0 0 0 0 0 - OK +TSS92 q1 0 0 0 0 0 - OK +TSS92 q2 0 0 0 0 0 - OK +TSS93 q1 0 0 0 0 0 - OK +TSS93 q2 0 0 0 0 0 - OK diff -r 000000000000 -r 21d03c46f286 test-data/var_model.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/var_model.tabular Thu Apr 02 16:13:37 2015 -0400 @@ -0,0 +1,175 @@ +condition locus compatible_count_mean compatible_count_var total_count_mean total_count_var fitted_var +q1 chr1:3111449-3111490 0.485913 0.472222 4.92956 0.00992266 0.485913 +q1 chr1:3111545-3111576 0 0 0.971825 1.88889 0 +q1 chr1:3174765-3174792 0 0 18.8169 76.4623 0 +q1 chr1:3187401-3187428 0 0 7.87321 1.52501 0 +q1 chr1:3188521-3188548 0 0 1.47183 0.445238 0 +q1 chr1:3189810-3190789 76.1899 402.705 81.0913 517.858 451.477 +q1 chr1:3190858-3191434 34.4929 0.485813 39.4083 3.9668 219.499 +q1 chr1:3191512-3192077 51.5139 545.417 58.8167 1041.2 313.521 +q1 chr1:3192250-3192336 0.985913 0.000396906 6.84504 29.5687 1.73488 +q1 chr1:3192441-3192494 1.45774 4.25 2.42956 11.8056 4.08367 +q1 chr1:3192550-3192629 0.485913 0.472222 1.47183 0.445238 0.485913 +q1 chr1:3192649-3192676 0 0 1 2 0 +q1 chr1:3192731-3192811 0 0 1.47183 0.445238 0 +q1 chr1:3192940-3193042 1.94365 7.55556 2.42956 11.8056 5.96791 +q1 chr1:3194185-3194226 0.485913 0.472222 2.94365 1.78095 0.485913 +q1 chr1:3194302-3194329 0 0 0.485913 0.472222 0 +q1 chr1:3194706-3194733 0 0 1 2 0 +q1 chr1:3195083-3195110 0 0 1.95774 1.83452 0 +q1 chr1:3195450-3195477 0 0 1.45774 4.25 0 +q1 chr1:3197089-3197116 0 0 1.47183 0.445238 0 +q1 chr1:3197246-3197273 0 0 0.485913 0.472222 0 +q1 chr1:3197346-3197373 0 0 0.485913 0.472222 0 +q1 chr1:3197425-3197452 0 0 1 2 0 +q1 chr1:3200022-3200191 2.95774 0.00357216 5.40139 3.92778 10.3101 +q1 chr1:3200325-3200352 0 0 0.971825 1.88889 0 +q1 chr1:3200430-3200457 0 0 1 2 0 +q1 chr1:3201007-3201039 0 0 3.44365 0.393652 0 +q1 chr1:3201077-3201481 8.78869 67.0179 9.2746 78.7413 48.9456 +q1 chr1:3201596-3201666 1 2 2.45774 0.419048 1.78395 +q1 chr1:3201672-3201699 0 0 0 0 0 +q1 chr1:3201725-3201809 2 8 2 8 6.18584 +q1 chr1:3204754-3204833 0.971825 1.88889 2.91548 17 1.66607 +q1 chr1:3211521-3211561 0 0 3.47183 4.67064 0 +q1 chr1:3212213-3212292 0.971825 1.88889 0.971825 1.88889 1.66607 +q1 chr1:3212367-3212439 1.94365 7.55556 2.42956 11.8056 5.96791 +q1 chr1:3212717-3212801 0.5 0.5 1 2 0.5 +q1 chr1:3213095-3213242 1.98591 2.05675 1.98591 2.05675 6.13133 +q1 chr1:3240606-3240633 0 0 2.95774 0.00357216 0 +q1 chr1:3242479-3242512 0 0 1.5 4.5 0 +q1 chr1:3242633-3242923 4.87321 30.0036 6.35913 22.5675 22.6559 +q1 chr1:3242924-3243005 0 0 1 2 0 +q1 chr1:3243018-3243079 0.971825 1.88889 0.971825 1.88889 1.66607 +q1 chr1:3243108-3243154 0.5 0.5 1 2 0.5 +q1 chr1:3243347-3243401 0.971825 1.88889 0.971825 1.88889 1.66607 +q1 chr1:3254079-3254106 0 0 5.95774 18.5107 0 +q1 chr1:3256974-3257011 0.971825 1.88889 2.94365 1.78095 1.66607 +q1 chr1:3277155-3277182 0 0 6.90139 0.0194484 0 +q1 chr1:3277190-3277218 0 0 1.45774 4.25 0 +q1 chr1:3277913-3278390 8.45774 61.4333 9.95774 99.1869 46.8827 +q1 chr1:3280117-3280144 0 0 5.97183 32.4524 0 +q1 chr1:3280498-3280525 0 0 0.985913 0.000396906 0 +q1 chr1:3280686-3280741 0.485913 0.472222 0.971825 1.88889 0.485913 +q1 chr1:3282504-3282531 0 0 1 2 0 +q1 chr1:3282650-3282677 0 0 0 0 0 +q1 chr1:3282760-3282832 0 0 1.48591 0.528572 0 +q1 chr1:3284966-3284993 0 0 2 8 0 +q1 chr1:3290488-3290553 0.485913 0.472222 2.47183 0.557937 0.485913 +q1 chr1:3290798-3290859 0.5 0.5 2.48591 4.58492 0.5 +q1 chr1:3290919-3291273 6.45774 25.0952 7.95774 50.8488 33.3712 +q1 chr1:3299443-3299664 2.98591 8.1131 5.91548 0.0142886 10.4193 +q1 chr1:3299691-3299733 0 0 0.5 0.5 0 +q1 chr1:3300051-3300078 0 0 0.5 0.5 0 +q1 chr1:3307748-3307775 0 0 2 8 0 +q1 chr1:3318620-3318647 0 0 3 18 0 +q1 chr1:3318999-3319051 0 0 0.5 0.5 0 +q1 chr1:3330527-3330554 0 0 4 32 0 +q1 chr1:3351240-3351311 0.5 0.5 13.5 364.5 0.5 +q1 chr1:3355887-3356119 2 8 2.5 12.5 6.18584 +q1 chr1:3356180-3356225 0.5 0.5 0.5 0.5 0.5 +q1 chr1:3363076-3363176 1 2 4.5 40.5 1.78395 +q1 chr1:3363214-3363278 0 0 0 0 0 +q1 chr1:3363387-3363446 1.5 4.5 1.5 4.5 4.24692 +q1 chr1:3363753-3363849 0 0 0.5 0.5 0 +q1 chr1:3364871-3364919 0.5 0.5 2.5 12.5 0.5 +q1 chr1:3367135-3367162 0 0 0.5 0.5 0 +q1 chr1:3367210-3367237 0 0 1 2 0 +q1 chr1:3367333-3367382 0 0 0 0 0 +q1 chr1:3369580-3369607 0 0 1 2 0 +q1 chr1:3375001-3375028 0 0 0 0 0 +q1 chr1:3377211-3377262 0 0 0.5 0.5 0 +q1 chr1:3379888-3379915 0 0 1.5 4.5 0 +q1 chr1:3386739-3386836 0 0 3 18 0 +q1 chr1:3391325-3391352 0 0 0 0 0 +q1 chr1:3435841-3435880 0 0 0 0 0 +q1 chr1:3447761-3447788 0 0 0 0 0 +q1 chr1:3450906-3450965 0 0 0 0 0 +q1 chr1:3451051-3451109 0 0 0 0 0 +q2 chr1:3111449-3111490 0.485913 0.472222 4.92956 0.00992266 0.485913 +q2 chr1:3111545-3111576 0 0 0.971825 1.88889 0 +q2 chr1:3174765-3174792 0 0 18.8169 76.4623 0 +q2 chr1:3187401-3187428 0 0 7.87321 1.52501 0 +q2 chr1:3188521-3188548 0 0 1.47183 0.445238 0 +q2 chr1:3189810-3190789 76.1899 402.705 81.0913 517.858 451.477 +q2 chr1:3190858-3191434 34.4929 0.485813 39.4083 3.9668 219.499 +q2 chr1:3191512-3192077 51.5139 545.417 58.8167 1041.2 313.521 +q2 chr1:3192250-3192336 0.985913 0.000396906 6.84504 29.5687 1.73488 +q2 chr1:3192441-3192494 1.45774 4.25 2.42956 11.8056 4.08367 +q2 chr1:3192550-3192629 0.485913 0.472222 1.47183 0.445238 0.485913 +q2 chr1:3192649-3192676 0 0 1 2 0 +q2 chr1:3192731-3192811 0 0 1.47183 0.445238 0 +q2 chr1:3192940-3193042 1.94365 7.55556 2.42956 11.8056 5.96791 +q2 chr1:3194185-3194226 0.485913 0.472222 2.94365 1.78095 0.485913 +q2 chr1:3194302-3194329 0 0 0.485913 0.472222 0 +q2 chr1:3194706-3194733 0 0 1 2 0 +q2 chr1:3195083-3195110 0 0 1.95774 1.83452 0 +q2 chr1:3195450-3195477 0 0 1.45774 4.25 0 +q2 chr1:3197089-3197116 0 0 1.47183 0.445238 0 +q2 chr1:3197246-3197273 0 0 0.485913 0.472222 0 +q2 chr1:3197346-3197373 0 0 0.485913 0.472222 0 +q2 chr1:3197425-3197452 0 0 1 2 0 +q2 chr1:3200022-3200191 2.95774 0.00357216 5.40139 3.92778 10.3101 +q2 chr1:3200325-3200352 0 0 0.971825 1.88889 0 +q2 chr1:3200430-3200457 0 0 1 2 0 +q2 chr1:3201007-3201039 0 0 3.44365 0.393652 0 +q2 chr1:3201077-3201481 8.78869 67.0179 9.2746 78.7413 48.9456 +q2 chr1:3201596-3201666 1 2 2.45774 0.419048 1.78395 +q2 chr1:3201672-3201699 0 0 0 0 0 +q2 chr1:3201725-3201809 2 8 2 8 6.18584 +q2 chr1:3204754-3204833 0.971825 1.88889 2.91548 17 1.66607 +q2 chr1:3211521-3211561 0 0 3.47183 4.67064 0 +q2 chr1:3212213-3212292 0.971825 1.88889 0.971825 1.88889 1.66607 +q2 chr1:3212367-3212439 1.94365 7.55556 2.42956 11.8056 5.96791 +q2 chr1:3212717-3212801 0.5 0.5 1 2 0.5 +q2 chr1:3213095-3213242 1.98591 2.05675 1.98591 2.05675 6.13133 +q2 chr1:3240606-3240633 0 0 2.95774 0.00357216 0 +q2 chr1:3242479-3242512 0 0 1.5 4.5 0 +q2 chr1:3242633-3242923 4.87321 30.0036 6.35913 22.5675 22.6559 +q2 chr1:3242924-3243005 0 0 1 2 0 +q2 chr1:3243018-3243079 0.971825 1.88889 0.971825 1.88889 1.66607 +q2 chr1:3243108-3243154 0.5 0.5 1 2 0.5 +q2 chr1:3243347-3243401 0.971825 1.88889 0.971825 1.88889 1.66607 +q2 chr1:3254079-3254106 0 0 5.95774 18.5107 0 +q2 chr1:3256974-3257011 0.971825 1.88889 2.94365 1.78095 1.66607 +q2 chr1:3277155-3277182 0 0 6.90139 0.0194484 0 +q2 chr1:3277190-3277218 0 0 1.45774 4.25 0 +q2 chr1:3277913-3278390 8.45774 61.4333 9.95774 99.1869 46.8827 +q2 chr1:3280117-3280144 0 0 5.97183 32.4524 0 +q2 chr1:3280498-3280525 0 0 0.985913 0.000396906 0 +q2 chr1:3280686-3280741 0.485913 0.472222 0.971825 1.88889 0.485913 +q2 chr1:3282504-3282531 0 0 1 2 0 +q2 chr1:3282650-3282677 0 0 0 0 0 +q2 chr1:3282760-3282832 0 0 1.48591 0.528572 0 +q2 chr1:3284966-3284993 0 0 2 8 0 +q2 chr1:3290488-3290553 0.485913 0.472222 2.47183 0.557937 0.485913 +q2 chr1:3290798-3290859 0.5 0.5 2.48591 4.58492 0.5 +q2 chr1:3290919-3291273 6.45774 25.0952 7.95774 50.8488 33.3712 +q2 chr1:3299443-3299664 2.98591 8.1131 5.91548 0.0142886 10.4193 +q2 chr1:3299691-3299733 0 0 0.5 0.5 0 +q2 chr1:3300051-3300078 0 0 0.5 0.5 0 +q2 chr1:3307748-3307775 0 0 2 8 0 +q2 chr1:3318620-3318647 0 0 3 18 0 +q2 chr1:3318999-3319051 0 0 0.5 0.5 0 +q2 chr1:3330527-3330554 0 0 4 32 0 +q2 chr1:3351240-3351311 0.5 0.5 13.5 364.5 0.5 +q2 chr1:3355887-3356119 2 8 2.5 12.5 6.18584 +q2 chr1:3356180-3356225 0.5 0.5 0.5 0.5 0.5 +q2 chr1:3363076-3363176 1 2 4.5 40.5 1.78395 +q2 chr1:3363214-3363278 0 0 0 0 0 +q2 chr1:3363387-3363446 1.5 4.5 1.5 4.5 4.24692 +q2 chr1:3363753-3363849 0 0 0.5 0.5 0 +q2 chr1:3364871-3364919 0.5 0.5 2.5 12.5 0.5 +q2 chr1:3367135-3367162 0 0 0.5 0.5 0 +q2 chr1:3367210-3367237 0 0 1 2 0 +q2 chr1:3367333-3367382 0 0 0 0 0 +q2 chr1:3369580-3369607 0 0 1 2 0 +q2 chr1:3375001-3375028 0 0 0 0 0 +q2 chr1:3377211-3377262 0 0 0.5 0.5 0 +q2 chr1:3379888-3379915 0 0 1.5 4.5 0 +q2 chr1:3386739-3386836 0 0 3 18 0 +q2 chr1:3391325-3391352 0 0 0 0 0 +q2 chr1:3435841-3435880 0 0 0 0 0 +q2 chr1:3447761-3447788 0 0 0 0 0 +q2 chr1:3450906-3450965 0 0 0 0 0 +q2 chr1:3451051-3451109 0 0 0 0 0