def testBuildVariantID(self): """ Tests creation of variant id from chrX:start-stop, ref_base, var_base or chrX:start, ref_base, var_base """ data1=['chrX:12321', 'A', 'T'] data2=['chrX:1234-1256', 'G', 'C'] result01=build_variant_id(data1) result02=build_variant_id(data2) self.assertEquals(result01, 'X_12321_12321_A_T') self.assertEquals(result02, 'X_1234_1256_G_C')
def add_links(Reader, sheet, fname): """ Process analysis file to add link columns """ #Need to get the pfx from the fname (f_path, f_name) = os.path.split(fname) f_short_name = f_name.replace('.SNP_Analysis.txt', '') #rowx is the row#, row is the data for rowx, row in enumerate(Reader): variant_id, ref_reads, var_reads = build_variant_id(row) row.insert(0, variant_id) for colx, value in enumerate(row): if colx == 0 and not value == 'gendb_link': if len(value) < 198: sheet.write_formula( rowx, colx, 'HYPERLINK("https://gendb.labmed.uw.edu/genetics_db/search?variant_id={}","gendb_link")' .format(value)) elif colx == 15 and not value == 'Faves_Y/N': if len(value) < 198: sheet.write_formula( rowx, colx, 'HYPERLINK("https://control.labmed.uw.edu/var_clin/fav/?variant_id={}&pfx={}&ref_reads={}&var_reads={}","mark_fav")' .format(variant_id, f_short_name, ref_reads, var_reads)) else: sheet.write(rowx, colx, float_if_possible(value))
def variant_id_link(Reader, sheet): """ Process analysis file to add link column """ for rowx, row in enumerate(Reader): row.insert(0, build_variant_id(row)) for colx, value in enumerate(row): if colx == 0 and not value == 'link': if len(value) < 198: sheet.write_formula(rowx, colx, 'HYPERLINK("https://apps.labmed.uw.edu/genetics_db/search?variant_id={}","link")'.format(value)) else: sheet.write(rowx, colx, float_if_possible(value))
def testBuildVariantID(self): """ Tests creation of variant id and read count from chrX:start-stop, ref_base, var_base or chrX:start, ref_base, var_base """ #A bunch of empty 'columns' to represent the data in the SNP tab data1 = [ 'chrX:12321', 'A', 'T', '', '', '', '', '', '', '', '', '', '', '', '', '10', '11' ] data2 = [ 'chrX:1234-1256', 'G', 'C', '', '', '', '', '', '', '', '', '', '', '', '', '12', '13' ] result01, ref_reads01, varreads01 = ann.build_variant_id(data1) result02, ref_reads02, varreads02 = ann.build_variant_id(data2) self.assertListEqual([result01, ref_reads01, varreads01], ['X_12321_12321_A_T', '10', '11']) self.assertListEqual([result02, ref_reads02, varreads02], ['X_1234_1256_G_C', '12', '13'])
def variant_id_link(Reader, sheet): """ Process analysis file to add link column """ for rowx, row in enumerate(Reader): row.insert(0, build_variant_id(row)) for colx, value in enumerate(row): if colx == 0 and not value == 'link': if len(value) < 198: sheet.write_formula( rowx, colx, 'HYPERLINK("https://apps.labmed.uw.edu/genetics_db/search?variant_id={}","link")' .format(value)) else: sheet.write(rowx, colx, float_if_possible(value))
def add_links(Reader, sheet, fname): """ Process analysis file to add link columns """ #Need to get the pfx from the fname (f_path, f_name) = os.path.split(fname) f_short_name = f_name.replace('.SNP_Analysis.txt','') #rowx is the row#, row is the data for rowx, row in enumerate(Reader): variant_id, ref_reads, var_reads=build_variant_id(row) row.insert(0, variant_id) for colx, value in enumerate(row): if colx == 0 and not value == 'gendb_link': if len(value) < 198: sheet.write_formula(rowx, colx, 'HYPERLINK("https://apps.labmed.uw.edu/genetics_db/search?variant_id={}","gendb_link")'.format(value)) elif colx == 15 and not value == 'Faves_Y/N': if len(value) < 198: sheet.write_formula(rowx, colx, 'HYPERLINK("https://kaos.labmed.uw.edu/var_clin/fav/?variant_id={}&pfx={}&ref_reads={}&var_reads={}","mark_fav")'.format(variant_id, f_short_name, ref_reads, var_reads)) else: sheet.write(rowx, colx, float_if_possible(value))