def test_get_introns(self): XKR8_uid = get_all_transcripts("XKR8", "grch38")[0]["qualifiers"]["uid"] transcript = Transcript(XKR8_uid, "grch38") introns = transcript.get_introns() intron_seq = transcript.get_seq_from_pos(introns) self.assertEqual( intron_seq, "GTGAGTGCTTCGCCCCGGGAGGGGAGGAGTGTCGGAGCCCAGCACCTCCGTCAGCTGGGTCACCTGTACAGGTGACACGCCATATGCCGGGAAGGGGACTGGGAGAGGGAACCAAGTCCTGTGGGCGCCTGGCCTACAGGTGAGCGTGCAGCCCTTTACGGAAAGGGAATCCCGGTAGACTGCCTTCATTCTAGCCCTAGCTTTCCTGGCACAGGCGAAGAAACTGAGGCCCAGGGAAGAAAGGGAGGCGCATGGGCTTTGAAGTCGGACCTCTCAGGGATCCACTTCTGGCTTTGCCCCCTCTCGCCTCACTTCTGCATTTCTCTGAGCCTCAGTTTCCTCCTGCGTAGAAAGGAGGTAGTCACCCTGAGACAGGTGTGACGGGCAGGCCTGTTGTGAAGAGTGAGCGAAAGAATGAGAAAGTGCCTCGCACAGTGCCTGGCCTGTAATGGCAGGGGCTGCGGACTCAGTTCAGCATCCCATGTTTCAGCATGGGCAGGGCCTTGGGAAGTCACTGACCTCTCAGTGGGGCTGTTTGGTTGCTGTTCCCATTGGGATGGGGATAGCGCCTGCCCGTTTGGTGAAGATGCAGTGAAATGACATCTGTCCACTGCCCTGGCTCAGAGTGAGCACTCAGCAACCTCAGCTGGCTTCTTGACCTGGGCCTCCCTGGGAGTTTCAGCAGCCCTGACCCCACCACAGCGCTTGCCCCTCACAAAGGCCGCCTCTCACCCTGTCTGCCTGGTTGTATTCTTCCCCCTGAAACTTGGCTTCCCACCCCAGACCCAGCAAGAGGGCAGAGATGGCCTCTGACTCATCCATGCCCATGGAGCCAGCCAGGGCTGGGCATAGGCTGGGTCCTGGAAAATGTGTGTGGATTCTGCTCCTTTTTGGACCTGGTGGAGCCTCGTAGAGATGGGAAAACAAACCCAAGGCTCAGAGGCATGCGACAAAGTCAGGGCAGAGGGTGGTGTGGGTTGGGATGGGGTGGCCAGGGCCAGGATCTGCTCTTGAATCCGTTTTTACAAACTCTTGAGATCTGGCCTTGACAAAGCCACACGGAGTCTCCAGGAGTGGAAGAGAGGAGCTTTGAATGTGGCAGTTTTGCCTGAGGGATTATAGAGACATCAGAAAACCCCGGGTGGGCATGAAGGGGTGCAGTTGTTAAGTCCTGGGCAGGCCTCCATGAGCCGTGAATCTGTAACTACCTTATGCATCTTTGTGGCCAATATTTCTGCTGAGCTTGAGTCAGACAGACTGTACTAGCTTTGGCTTTGGAAATGGGTCTCTGTTCCTGCCTGTGAATTGGCCGAGGCAGGGGTCCCTGCTAGGTCACTGGGGACCATAGGCAAAGGCTCCTGCTGAGGGAGAACCCCAGCCTGTCCTGCCTGCCTGCTCCTCAGTGTGTTCTTGTGTCCTTCCAGGGGAAGTGACAGTACATGTCTGGTGAATGAGCTTGTGATGAGTGAACGGGGTTCTCTCCCAATAGGCAACTGAGAGCAAAGTTCTGGGTGGAGGGTCCTTGGTGCATCCTCCACTTACTCTTCATGCCAGTGGGTACCCCAGACCTGTCTGTCCAAACTCTGGACTCTCTTAACTCCGCCCCAATCTCCATCCTTAACCACTCAGGGCCAGCCTCTTAAATGGGATCCCTCCTTCCAATCTAACCCTCCTCCAGCCCCTCCCCTGTGTGGCCGGGGCAAGGCAGAGTCTGATTCCATCTGGCCTGTGCCCAGAAGTGCCCAAGAGGCAAATGTCCTCTTGCCCACAGGACCCCAGGAGATCTTGGGCACACTAAAGTTTGAGAACTACTGCCTCAGGCAACTTTATAGCATGCCTTTCCAATTCAGGTTTGGATCCAAATCCTCATTCCAGTACTTATTAGCTGCTTATAATTTTTTGTTTGTTTTTTAAAAAGAGGTAGGGTCTGGTCAGGCTTGGTGGCTCATGCCTGTAATCCTAGCAGTCTGGGAGGCTGACGTGGGTGGATCACTTGAGGTCAGGAGTTTGAGACCAGCCTGCTGAACATGGCAAAAGCTCATCTCTACAAAAATTAGCCAGGTGTGGTGGCGCATGCCTGTAATCCCAGCATCCCAGCTACTCTGGAGGCCGAGGCAGGAGAATCGCTTGAACCTGGGAGGTGGAGGTTGCAGTGAGCCGAGTTTGTGCCACTGCACTCTAGCCTGGGCGACAAGCGACAGATGTAGACTCTGTCTCCAAAAAAAAAGAAAAAAAAAAAGAGAGAGAGAGGCAGGGTCTCTGTTGCCTGGGCTGGAGTGCAGTGGCACAATCAATCATGGCTCACAGTGGCCTTGAACTCCTGGGCTCAAGCTGTCCTCCTGCGTCAGCCTCCTGAGTAGCTTGGACTACAGGCTTGTACCACCACGTCCAACTAATTAAAAAAAATTCTTTGTAGAGATGGGGCTTGCTGTGTTGCCCAGGGTGGTCTCAAACTCCTGGCCTCCAGTGATCCTCTTGCCTTGGCCTGTCAAAATGTTGGGATTACAGGCGCGAGCCACTGCACCCAGACCTTATTAGCTTCTTGATCCTGTTTCCCCATCTGTAAAATGGGCTTTTGTGAGAAGTAAACAGGACAAGGTTTGTGATGAGCTTGGGACAGTGCTTAGCCAGCGGGAGTAGAAGGTGTATTGATCCCCATTTTTGCTTTTTTGTTTTTTTTGAGACGGAGTCTTGTTCTGTCGCCAGGCTGGAGTGCAGTGGCACGATCTCGGCTCACTGTAACCTCCGCCTTGCAGATTCAAGAGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGACTACAGGCGCGCACCACCACACCCAGCTAATTTTTTGTATTAGTAGAGACGAGGCTTCACCATGTTAGCCAGGATGGTCTCAATCTCCTGAACTCGTGATCAGCCCGCCTCAGACTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCACACCCGGCCTCGATCCTCATTTTACAGATGAAACAAGTTCAGTGAGGTTAGGACATTGCCGAAGGCCCCATAGCATGGATGTGAGGAGACAGGTTGGAGCCTGTGTCCACTCATTAGATGGGTGGGAGGCTGAGGAATTCACAGGACACTAACCTGGCCCTCTGGGCATTTGTGTGTGGTGCCTAGGTGAGTGAAGGCCTGTGGCTGGCCCCCCTGTCGTGGCTTGGTGGGGGGTCTCTCAAATGTTGGAACTGTTTTTAGTCTTTTATAAAGGCTGCTTAGAAAACAGGAGAACAGGCTTTAGTCAGGCAGATCTGGCTTGAAACCTAAAGTCACTCTACAGCTGTTTGAGTTTGGACAAATGCCTTGACCTCTCTGAGTATGTTTGTTCTCATCTGAAATATGGGCTTAAATCCTCCTGCCTCATAAGGTTGATGAAAGGATTAAATGAGGTGATGCAAAGAAAGCCCATTTCCTGGTACATAAGTTCCTGGTACAGAGTCTCACTCTGTCATCGCCCGTAGTGGAGTACAGCAGCCTGATCATGGCTCACTGTAGCCTCCACCTCCCAGGCTCAAGTGATCCTCCTGTCTCAGCCTCCTGAGTAGCTGGGACTACAAGTGTGTATCACCATGCTGGCTAATTTTTCTTTCTTTTTTTTTTTTTTTTTTTTGTAGAGACGAGGTCCCACTTTGTTACCCAGGCTGGTCTTGAACTCCTGAGCTCAAGTAACCTCCTACCTCAGCCTCCTAAGGTGCTGGGATTACAGGTGTCGCCCACTGTGCCTGGCCCACAAGTCTTAATTGTAATTTTTATAATTTTGAAGATAATGAAGTGTGTAAGGTGCCTGATACAGCATAGGTAACTTTTTAGTTAAGAAACAATTTCATACGTTGGGAGGCCAAGGTGCACAGGTCGCTTGAGGCCAGAGTTGGAGACCATCCTGGGTAACATAGTGAGACCTCATCTCTTCAAAATTTTAAAAGAGAAACAAGAAACAATATATTGAATGCCTTCATCCAGTCAGGTTTTCATTGTGCATCTCTTCTGTGCCTGTTACTGTGCTGGGGACACAGCAGTGAACAAGATGAACCCAGCCCCTGCCCTGCCAGGATGATAGACTAAAACAAGTAGCTACGGTTGAGTGACTGGAAAAGGGAGAGGCAGGGAGCAGAGGATCACAGGGCCCCCTAAGCATGGGTGAAGTTTACAGTGAGGAGCTTTGGGAGGGTTTTTGCATGAAAGGAAAGTGACTTGCCCATTTCCACAGACCTGGACAGTGGCCAAGCTAAAGAGGGCCCCCACTCACATCCGACTCAGGGTCCAAGCCTTCCCCTTTGCCTTCCTCCACCGCTGCCATAAATGCCACAGCCTCTCAAGAAACCAGTCCTCACTCTACCGTCACTCGCTGTGTGACCTGGAGAGCCTTCCTGTGGAAGATGGAGGTTGGACTCGATCTCCAAGGGCCCTTTCGTCTTGCTAGTCTGAGTCTATATATTGATTGAAAAAACAATAATAGCGGCTGTCACAATCGAGTGCCAGCTATTAGCCAGGCCCTGTGGGAAGCACTTACAGTCATCATTGCTCATGTTCACAGCAGCCCTGTAGGTTTGTGCTATATTGATCTTCATTTTTAAAGAGGTGCAGAAAGGTGAGTGACTTGCCCTGGGTTACTGGGCACTCACTGGGCACACGTCTTTGTCTGTTGAGGGTTGGGGGTGTCTAGAACCAGGGCCAAGTGCAGACAGTCTGCACTGTGAGTGTGGCAGGGGGTAAGGGGGCGAGACAGATTTTCCCTACTTTTTATTTAGCAAACATCTCTTTCGCTGCTGTTATGTGCCAGGTACTGGGCTGCTGGGGGATCCCAAGTGAGCAGAGTCTGTTTTCTACCCTCGAGGAGCCCAGAGATAAGGAAATAGATAATTACTGTGTGATGAGACTCCAGACAGAGGTGGGTGGCATGTTACAGGGATACCTGACACAGCTGAGTGGGTGGCATGGGGTCAGGGTGGGTGACTCCCGGGGCTCTTCAAGCTGGGGCCTGCGGGGTAATGGAGGAGTAGGCCGGGGAAGTGGGGCCTGTGCTTCTGGCGACCTAACATCCTGGGCAGAGCTTGTCAAGGTCACGGAAGGTGGCATGCTGGGCAAACTGGAAGAACATCAGCCCTGCTGAGACCTGGGCAAGGCTAATGAGCACAGATCTGTTTCCAGGCTAGGAGTGGGTTCTGGGCGCCTAATAGGTTCCCAGTAAACATCTGTCGAATGACTGCGGTGGACGGGGACAGGGGAGGAAGCAGTCGGGAGACGTGCCGGTGCCACTTCCATCCCTCCCTGGAGGCCCTTGTGCTTCTGCTCCAGGATTGGCAACCAGGAGGTGGGATAGGACCCCTGTTGTAAACTTCTGGATCTTGGAAAATCAAGGTTAGGGGTCAGTCCGATGGCCTCTGGTCTTGGAGGGGAGGGGAGGGGAGTGGGGAGACCTTCTGTCCACACAGCAGGGACATCTCTCCTGGCCCTGAGGGCAGCTTTAGCCAGAGCCTGTTGCCACCCCATGGGATTTTCTACTCCCTTTTTGAGACTAAGAAAGACGGAACTGAGACTGTTGATTTTTAGACACAAGGAAGGCTTGTGTTCTTCCCAGAAAGAAAGGGTTATGGGGCCCTGGAAGATGCCCAGGATGCAGCCAAGGCCCAGGGGTGCTGAGTGCTGGGTGGGCCACAGGTCACATCCTCTCATCTTTGACAAATACCACCCGGATAGCACCTACGCAGCAAAGCGCTGTGGTGAGGGGCAGGCTCTATATTAGGAGTCATAGCTTTGTTTTTGGTTGTGGGAACTCACTGGGTCTTCTCTAGCTGCAGATTTGCCTTCAACAAACGAGGGATTCTAATACCTACCCCAGGGTTGCTGGGAGGGCCCCCACGGTACCTGTGACCGCTGGGGAGTGCCAAGCAGGCTGGCCCCAGGACTCACTGTTCCCTCCTACTCTTTGCAG" .upper())
def test_noncoding_gene(self): PRDM15_uid = get_all_transcripts("PRDM15", "grch38")[0]["qualifiers"]["uid"] transcript = Transcript(PRDM15_uid, "grch38") exons = transcript.get_coding() exon_seq = transcript.get_seq_from_pos(exons) self.assertEqual( exon_seq, "ATGGCTGAAGATGGGAGCGAAGAGATCATGTTCATCTGGTGTGAAGACTGCAGCCAGTACCACGACTCCGAATGTCCCGAGCTGGGCCCAGTGGTCATGGTCAAAGACTCCTTTGTGTTAAGCAGGGCAAGGTCATCCCTTCCTCCCAACTTGGAGATCAGACGACTGGAAGATGGAGCCGAGGGGGTGTTCGCCATCACTCAGCTCGTCAAGCGGACACAGTTCGGTCCCTTTGAGTCCAGGAGGGTCGCCAAATGGGAAAAGGAGTCTGCATTTCCCCTGAAGGTGTTCCAGAAGGACGGGCACCCCGTGTGCTTCGACACCTCCAACGAGGATGACTGCAACTGGATGATGCTGGTGCGGCCAGCGGCGGAGGCCGAGCACCAGAACCTGACGGCCTACCAGCACGGCAGCGACGTGTACTTCACCACCTCCAGAGACATCCCCCCGGGTACCGAGCTGCGCGTGTGGTATGCGGCCTTCTATGCCAAGAAGATGGACAAGCCCATGCTGAAGCAGGCCGGCTCTGGCGTCCACGCTGCAGGCACCCCAGAAAACAGCGCCCCCGTGGAGTCGGAGCCCAGCCAGTGGGCGTGTAAAGTGTGTTCTGCCACCTTCCTGGAGCTGCAGCTCCTCAATGAACATCTGTTGGGCCACTTAGAACAAGCCAAAAGCCTTCCTCCAGGCAGCCAAAGCGAGGCAGCAGCTCCCGAGAAGGAGCAGGACACACCCCGGGGGGAACCCCCTGCAGTGCCCGAGAGCGAGAATGTTGCCACCAAAGAACAGAAGAAAAAGCCTCGAAGGGGGAGAAAACCCAAAGTGTCCAAAGCTGAGCAGCCTCTAGTCATCGTGGAAGACAAGGAACCCACAGAGCAAGTGGCAGAGATCATTACCGAGGTCCCTCCGGATGAGCCTGTGAGTGCAACGCCAGATGAGCGGATCATGGAGCTGGTTCTGGGGAAGCTGGCCACCACCACCACTGACACCAGCTCGGTTCCAAAGTTCACCCATCATCAGAATAACACCATCACGCTCAAGAGGAGCTTAATTCTCTCAAGCAGACACGGCATCCGGCGCAAGCTCATCAAACAGCTCGGGGAGCACAAGCGGGTTTACCAGTGCAATATCTGCAGCAAGATCTTCCAGAACAGCAGCAACCTGAGCAGGCACGTGCGCTCGCATGGTGACAAGCTGTTTAAGTGCGAAGAGTGTGCAAAATTGTTCAGCCGCAAAGAGAGCCTAAAGCAGCACGTTTCCTACAAGCACAGCAGGAACGAGGTGGACGGCGAGTACAGGTACCGCTGCGGCACTTGTGAGAAGACCTTCCGCATCGAGAGCGCGCTGGAGTTCCACAACTGCAGGACAGATGACAAGACGTTCCAATGTGAGATGTGTTTCAGATTCTTCTCCACCAACAGCAACCTCTCCAAGCACAAGAAGAAGCACGGCGACAAGAAGTTTGCCTGTGAGGTCTGCAGCAAGATGTTCTACCGCAAGGACGTCATGCTGGACCACCAGCGCCGGCACCTGGAAGGAGTGCGGCGAGTGAAGCGAGAGGACCTGGAGGCCGGTGGGGAGAACCTGGTCCGTTACAAGAAGGAGCCTTCCGGGTGCCCGGTGTGTGGCAAGGTGTTCTCCTGCCGGAGCAATATGAACAAGCACCTGCTCACCCACGGCGACAAGAAGTACACCTGCGAGATCTGCGGGCGCAAGTTCTTCCGCGTGGATGTGCTCAGGGACCACATCCATGTCCACTTCAAGGACATCGCGTTGATGGATGACCACCAGAGGGAAGAGTTTATCGGCAAGATCGGGATCTCCTCGGAAGAAAACGATGACAATTCTGACGAGAGCGCAGACTCGGAGCCTCACAAGTACAGCTGCAAGCGGTGCCAGCTCACCTTCGGCCGGGGGAAGGAGTACCTGAAGCACATCATGGAGGTGCACAAGGAGAAGGGCTATGGCTGCAGCATCTGCAACCGGCGCTTTGCACTGAAGGCCACCTACCACGCCCACATGGTCATCCACCGTGAAAACCTGCCGGACCCCAACGTGCAGAAGTACATCCACCCCTGCGAGATCTGCGGGCGGATCTTCAACAGCATCGGGAACCTGGAGCGCCACAAGCTCATCCACACAGGTGTGAAGAGCCACGCCTGCGAGCAGTGTGGGAAGTCCTTTGCCAGGAAGGACATGCTGAAGGAGCACATGCGTGTGCACGACAATGTCCGCGAGTACCTGTGTGCCGAGTGTGGGAAAGGCATGAAGACCAAGCACGCGCTGCGCCACCACATGAAGCTGCACAAGGGCATCAAGGAGTACGAGTGCAAGGAGTGCCACCGCAGGTTCGCGCAGAAGGTCAACATGCTCAAGCACTGCAAGCGGCACACGGGGATTAAAGATTTCATGTGTGAATTGTGTGGGAAGACATTCAGCGAGAGGAACACCATGGAGACCCACAAGCTCATCCACACAGTGGGCAAGCAGTGGACGTGCTCCGTGTGCGACAAGAAGTACGTGACCGAGTACATGCTGCAGAAGCACGTTCAGCTCACACACGACAAGGTGGAGGCGCAGAGCTGCCAGCTGTGCGGGACCAAGGTGTCCACCAGGGCCTCCATGAGCCGACACATGCGGCGCAAGCACCCCGAGGTGCTCGCGGTGAGGATCGATGACCTGGACCACCTCCCGGAGACCACCACCATCGACGCCTCCTCCATTGGCATCGTCCAGCCTGAGCTGACTCTGGAGCAGGAGGATTTGGCCGAAGGGAAGCACGGGAAAGCTGCCAAGCGAAGTCACAAGAGAAAGCAGAAGCCAGAAGAGGAGGCGGGTGCTCCGGTGCCCGAGGACGCCACCTTCAGCGAATACTCAGAGAAAGAGACGGAGTTCACAGGCAGTGTAGGCGACGAGACCAATTCCGCAGTACAGAGCATTCAGCAGGTAGTGGTGACCCTGGGTGACCCAAATGTGACCACACCATCGAGCTCAGTCGGCTTAACCAACATCACCGTGACCCCCATCACCACTGCGGCCGCGACTCAGTTTACCAATCTCCAGCCGGTGGCCGTGGGGCACCTTACCACCCCTGAACGCCAGTTACAGCTGGACAACTCAATCCTGACCGTGACCTTTGATACCGTCAGCGGCTCTGCCATGTTGCACAACCGCCAAAATGACGTCCAGATCCACCCCCAGCCGGAAGCCTCGAACCCACAGTCTGTGGCCCATTTCATCAACCTGACGACCCTGGTCAACTCCATCACGCCCCTGGGGAGCCAGCTTAGTGACCAGCACCCGCTCACGTGGCGGGCAGTGCCCCAGACTGACGTCTTGCCACCCTCGCAGCCGCAGGCACCCCCACAGCAGGCGGCCCAGCCCCAGGTGCAGGCGGAGCAGCAGCAGCAGCAGATGTACAGCTACTGA" )
def test_get_coding_negative_exons(self): TOR1A_uid = get_all_transcripts("TOR1A", "grch38")[0]["qualifiers"]["uid"] transcript = Transcript(TOR1A_uid, "grch38") exons = transcript.get_coding() exon_seq = transcript.get_seq_from_pos(exons) self.assertEqual( exon_seq, "ATGAAGCTGGGCCGGGCCGTGCTGGGCCTGCTGCTGCTGGCGCCGTCCGTGGTGCAGGCGGTGGAGCCCATCAGCCTGGGACTGGCCCTGGCCGGCGTCCTCACCGGCTACATCTACCCGCGTCTCTACTGCCTCTTCGCCGAGTGCTGCGGGCAGAAGCGGAGCCTTAGCCGGGAGGCACTGCAGAAGGATCTGGACGACAACCTCTTTGGACAGCATCTTGCAAAGAAAATCATCTTAAATGCCGTGTTTGGTTTCATAAACAACCCAAAGCCCAAGAAACCTCTCACGCTCTCCCTGCACGGGTGGACAGGCACCGGCAAAAATTTCGTCAGCAAGATCATCGCAGAGAATATTTACGAGGGTGGTCTGAACAGTGACTATGTCCACCTGTTTGTGGCCACATTGCACTTTCCACATGCTTCAAACATCACCTTGTACAAGGATCAGTTACAGTTGTGGATTCGAGGCAACGTGAGTGCCTGTGCGAGGTCCATCTTCATATTTGATGAAATGGATAAGATGCATGCAGGCCTCATAGATGCCATCAAGCCTTTCCTCGACTATTATGACCTGGTGGATGGGGTCTCCTACCAGAAAGCCATGTTCATATTTCTCAGCAATGCTGGAGCAGAAAGGATCACAGATGTGGCTTTGGATTTCTGGAGGAGTGGAAAGCAGAGGGAAGACATCAAGCTCAAAGACATTGAACACGCGTTGTCTGTGTCGGTTTTCAATAACAAGAACAGTGGCTTCTGGCACAGCAGCTTAATTGACCGGAACCTCATTGATTATTTTGTTCCCTTCCTCCCCCTGGAATACAAACACCTAAAAATGTGTATCCGAGTGGAAATGCAGTCCCGAGGCTATGAAATTGATGAAGACATTGTAAGCAGAGTGGCTGAGGAGATGACATTTTTCCCCAAAGAGGAGAGAGTTTTCTCAGATAAAGGCTGCAAAACGGTGTTCACCAAGTTAGATTATTACTACGATGATTGA" )
def test_get_utrs_negative_strand(self): TOR1A_uid = get_all_transcripts("TOR1A", "grch38")[0]["qualifiers"]["uid"] transcript = Transcript(TOR1A_uid, "grch38") both_utr = transcript.get_utr("both") both_utr = transcript.get_seq_from_pos(both_utr) self.assertEqual( both_utr, "GCACCGGTTCGCGGTCGGCGCGAGAACAAGCAGGGTGGCGCGGGTCCGGGCCAGTCATGATTGGCAGCCGGAGTCACTGCCTGGAGTTGGAAAAGAAACAACACTCAGTCCTTCCACACTTCCACCCCCAGCTCCTTTCCCTGGAAGAGGAATCCAGTGAATGTTCCTGTTTGATGTGACAGGAATTCTCCCTGGCATTGTTTCCACCCCCTGGTGCCTGCAGGCCACCCAGGGACCACGGGCGAGGACGTGAAGCCTCCCGAACACGCACAGAAGGAAGGAGCCAGCTCCCAGCCCACTCATCGCAGGGCTCATGATTTTTTACAAATTATGTTTTAATTCCAAGTGTTTCTGTTTCAAGGAAGGATGAATAAGTTTTATTGAAAATGTGGTAACTTTATTTAAAATGATTTTTAACATTATGAGAGACTGCTCAGATTCTAAGTTGTTGGCCTTGTGTGTGTGTTTTTTTTTAAGTTCTCATCATTATTACATAGACTGTGATGTATCTTTACTGGAAATGAGCCCAAGCACACATGCATGGCATTTGTTCCACAGGAGGGCATCCCTGGGGATGTGGCTGGAGCATGAGCCAGCTCTGTCCCAGGATGGTCCCAGCGGATGCTGCCAGGGGCAGTGAAGTGTTTAGGTGAAGGACAAGTAGGTAAGAGGACGCCTTCAGGCACCACAGATAAGCCTGAAACAGCCTCTCCAAGGGTTTTCACCTTAGCAACAATGGGAGCTGTGGGAGTGATTTTGGCCACACTGTCAACATTTGTTAGAACCAGTCTTTTGAAAGAAAAGTATTTCCAACTTGTCACTTGCCAGTCACTCCGTTTTGCAAAAGGTGGCCCTTCACTGTCCATTCCAAATAGCCCACACGTGCTCTCTGCTGGATTCTAAATTATGTGAATTTTGCCATATTAAATCTTCCTCATTTATACTATTATTTGTTACGTTCAATCAGAATCCCCGAAACCTCCTATAAAGCTTAGCTGCCCCTTCTGAGGATGCTGAGAACGGTGTCTTTCTTTATAAATGCAAATGGCTACCGTTTTACAATAAAATTTTGCATGTGCCA" ) prime_5 = transcript.get_utr("5_prime") prime_5 = transcript.get_seq_from_pos(prime_5) self.assertEqual( prime_5, "GCACCGGTTCGCGGTCGGCGCGAGAACAAGCAGGGTGGCGCGGGTCCGGGC") prime_3 = transcript.get_utr("3_prime") prime_3 = transcript.get_seq_from_pos(prime_3) self.assertEqual( prime_3, "CAGTCATGATTGGCAGCCGGAGTCACTGCCTGGAGTTGGAAAAGAAACAACACTCAGTCCTTCCACACTTCCACCCCCAGCTCCTTTCCCTGGAAGAGGAATCCAGTGAATGTTCCTGTTTGATGTGACAGGAATTCTCCCTGGCATTGTTTCCACCCCCTGGTGCCTGCAGGCCACCCAGGGACCACGGGCGAGGACGTGAAGCCTCCCGAACACGCACAGAAGGAAGGAGCCAGCTCCCAGCCCACTCATCGCAGGGCTCATGATTTTTTACAAATTATGTTTTAATTCCAAGTGTTTCTGTTTCAAGGAAGGATGAATAAGTTTTATTGAAAATGTGGTAACTTTATTTAAAATGATTTTTAACATTATGAGAGACTGCTCAGATTCTAAGTTGTTGGCCTTGTGTGTGTGTTTTTTTTTAAGTTCTCATCATTATTACATAGACTGTGATGTATCTTTACTGGAAATGAGCCCAAGCACACATGCATGGCATTTGTTCCACAGGAGGGCATCCCTGGGGATGTGGCTGGAGCATGAGCCAGCTCTGTCCCAGGATGGTCCCAGCGGATGCTGCCAGGGGCAGTGAAGTGTTTAGGTGAAGGACAAGTAGGTAAGAGGACGCCTTCAGGCACCACAGATAAGCCTGAAACAGCCTCTCCAAGGGTTTTCACCTTAGCAACAATGGGAGCTGTGGGAGTGATTTTGGCCACACTGTCAACATTTGTTAGAACCAGTCTTTTGAAAGAAAAGTATTTCCAACTTGTCACTTGCCAGTCACTCCGTTTTGCAAAAGGTGGCCCTTCACTGTCCATTCCAAATAGCCCACACGTGCTCTCTGCTGGATTCTAAATTATGTGAATTTTGCCATATTAAATCTTCCTCATTTATACTATTATTTGTTACGTTCAATCAGAATCCCCGAAACCTCCTATAAAGCTTAGCTGCCCCTTCTGAGGATGCTGAGAACGGTGTCTTTCTTTATAAATGCAAATGGCTACCGTTTTACAATAAAATTTTGCATGTGCCA" )