def ens_genes_for(factor_name, pssm_map): return set( pssm_map[m] for m in set(str(m.acc) for m in transfac_factors.matrices_by_factor_name(factor_name)) if m in pssm_map )
def ens_genes_for(factor_name, pssm_map): return set(pssm_map[m] for m in set( str(m.acc) for m in transfac_factors.matrices_by_factor_name(factor_name)) if m in pssm_map)
'ATF', 'CREB', 'Arnt', 'YY1', ] """ The transcription factors in "Genome-Wide In Silico Identification of Transcriptional Regulators Controlling the Cell Cycle in Human Cells" Elkon et al. Table 3 """ elkon_tf_ens_genes = dict( (tf, ens_genes_for(tf, pssm_map)) for tf in elkon_tfs) raise for factor_name in elkon_tfs: print factor_name, ':', ','.join( set(m.name for m in transfac_factors.matrices_by_factor_name(factor_name))) open('elkon-cell-cycle-small-ensembl.txt', 'w').write('\n'.join('\n'.join(pssm_map[matrix]) for matrix in elkon_tfs_small.values())) open('elkon-cell-cycle-ensembl.txt', 'w').write('\n'.join('\n'.join(pssm_map[matrix]) for matrix in elkon_tfs.values())) #translated = S.translate('ensembl', 'H**o sapiens', 'unigene', 'ensembl_gene_id', [ 'Hs.239', 'Hs.715518', 'Hs.181768', 'Hs.427236' ]) #print 'Translated: %s' % ', '.join('->'.join(map(str, x)) for x in translated) def yield_refs(filename): """Yield references in filename""" f = open(file)
'NF-Y', 'NRF-1', 'ETF', 'ATF', 'CREB', 'Arnt', 'YY1', ] """ The transcription factors in "Genome-Wide In Silico Identification of Transcriptional Regulators Controlling the Cell Cycle in Human Cells" Elkon et al. Table 3 """ elkon_tf_ens_genes = dict((tf, ens_genes_for(tf, pssm_map)) for tf in elkon_tfs) raise for factor_name in elkon_tfs: print factor_name, ':', ','.join(set(m.name for m in transfac_factors.matrices_by_factor_name(factor_name))) open('elkon-cell-cycle-small-ensembl.txt', 'w').write('\n'.join('\n'.join(pssm_map[matrix]) for matrix in elkon_tfs_small.values())) open('elkon-cell-cycle-ensembl.txt', 'w').write('\n'.join('\n'.join(pssm_map[matrix]) for matrix in elkon_tfs.values())) #translated = S.translate('ensembl', 'H**o sapiens', 'unigene', 'ensembl_gene_id', [ 'Hs.239', 'Hs.715518', 'Hs.181768', 'Hs.427236' ]) #print 'Translated: %s' % ', '.join('->'.join(map(str, x)) for x in translated)