Python Transcript.get_coding Examples

Example #1

File: test_transcript.py Project: wassermanlab/GeneBreaker

 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"
     )

Example #2

File: test_transcript.py Project: wassermanlab/GeneBreaker

 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"
     )