def getGeneByRefTr(in_ref_tr, trim_version=True): """ Return gene object by RNA_id. :param in_ref_tr: Path to the file describing the link between genes and RNA_id (format: TSV). Each line has the following format: <GENE>\t<RNA_ID>. :type in_ref_tr: str :param trim_version: With True the version number is removed from the id. :type trim_version: boolean :return: The genes by RNA_id. :rtype: dict """ gene_by_tr = dict() with open(in_ref_tr) as FH_tr: for line in FH_tr: if not line.startswith("#"): gene, tr_id = [field.strip() for field in line.split("\t")] if tr_id != "": if trim_version: tr_id = tr_id.split(".")[0] gene_by_tr[tr_id] = Gene(name=gene) return gene_by_tr
def testGetTranscriptsAnnot_withoutUTR_threeExons(self): exon_1 = Exon(10, 40, "+", "chr1", "fwd_exon_1") exon_2 = Exon(91, 150, "+", "chr1", "fwd_exon_2") exon_3 = Exon(201, 361, "+", "chr1", "fwd_exon_3") cds_1 = CDS(10, 40, "+", "chr1", "fwd_cds_1") cds_2 = CDS(91, 150, "+", "chr1", "fwd_cds_2") cds_3 = CDS(201, 361, "+", "chr1", "fwd_cds_3") gene_1 = Gene(10, 350, None, "chr1", "gene_1", {"id": "g_1"}) transcrit_1 = Transcript(None, None, None, "chr1", "transcrit_1", {"id": "tr_1"}, parent=gene_1, children=[exon_1, exon_2, exon_3]) protein_1 = Protein(None, None, None, "chr1", "protein_1", children=[cds_1, cds_2, cds_3], transcript=transcrit_1) queries = [ Region(80, 100, None, "chr1", "query_1", {"desc": "starts before exon_2 ; ends in exon_2."}), Region(100, 180, None, "chr1", "query_2", {"desc": "starts in exon_2 ; ends after exon_2."}), Region( 91, 150, None, "chr1", "query_3", { "desc": "starts at the start of exon_2 ; ends at the end of exon_2." }), Region(80, 170, None, "chr1", "query_4", {"desc": "starts before exon_2 ; ends after exon_2."}), Region(80, 230, None, "chr1", "query_5", {"desc": "starts before exon_2 ; ends in exon_3."}), Region(100, 400, None, "chr1", "query_6", {"desc": "starts in exon_2 ; ends after exon_3."}), Region(100, 250, None, "chr1", "query_7", {"desc": "starts in exon_2 ; ends in exon_3."}), Region(80, 370, None, "chr1", "query_8", {"desc": "starts before exon_2 ; ends after exon_3."}), Region(90, 151, None, "chr1", "query_9", { "desc": "starts just before exon_2 ; ends just after exon_2." }) ] # Expected forward 3 exons expected = { "query_1": { "start_EXON": None, "start_INTRON": "1/2", "start_Protein_position": 11, "end_EXON": "2/3", "end_INTRON": None, "end_Protein_position": 14 }, "query_2": { "start_EXON": "2/3", "start_INTRON": None, "start_Protein_position": 14, "end_EXON": None, "end_INTRON": "2/2", "end_Protein_position": 31 }, "query_3": { "start_EXON": "2/3", "start_INTRON": None, "start_Protein_position": 11, "end_EXON": "2/3", "end_INTRON": None, "end_Protein_position": 31 }, "query_4": { "start_EXON": None, "start_INTRON": "1/2", "start_Protein_position": 11, "end_EXON": None, "end_INTRON": "2/2", "end_Protein_position": 31 }, "query_5": { "start_EXON": None, "start_INTRON": "1/2", "start_Protein_position": 11, "end_EXON": "3/3", "end_INTRON": None, "end_Protein_position": 41 }, "query_6": { "start_EXON": "2/3", "start_INTRON": None, "start_Protein_position": 14, "end_EXON": "3/3", "end_INTRON": None, "end_Protein_position": 84 }, "query_7": { "start_EXON": "2/3", "start_INTRON": None, "start_Protein_position": 14, "end_EXON": "3/3", "end_INTRON": None, "end_Protein_position": 47 }, "query_8": { "start_EXON": None, "start_INTRON": "1/2", "start_Protein_position": 11, "end_EXON": "3/3", "end_INTRON": None, "end_Protein_position": 84 }, "query_9": { "start_EXON": None, "start_INTRON": "1/2", "start_Protein_position": 11, "end_EXON": None, "end_INTRON": "2/2", "end_Protein_position": 31 }, } for query_name, query_res in expected.items(): for key, val in { "SYMBOL": "gene_1", "Gene": "g_1", "Feature": "tr_1", "Feature_type": "Transcript", "STRAND": "1" }.items(): query_res[key] = val # Apply forward strand for exon in transcrit_1.children: exon.strand = "+" for cds in protein_1.children: cds.strand = "+" transcrit_1.sortChildren() protein_1.sortChildren() # Assert for curr_query in queries: annotations = getTranscriptsAnnot(curr_query, [transcrit_1]) self.assertEqual([expected[curr_query.name]], annotations) # Expected reverse 3 exons expected = { "query_1": { "start_EXON": "2/3", "start_INTRON": None, "start_Protein_position": 71, "end_EXON": None, "end_INTRON": "2/2", "end_Protein_position": 74 }, "query_2": { "start_EXON": None, "start_INTRON": "1/2", "start_Protein_position": 54, "end_EXON": "2/3", "end_INTRON": None, "end_Protein_position": 71 }, "query_3": { "start_EXON": "2/3", "start_INTRON": None, "start_Protein_position": 54, "end_EXON": "2/3", "end_INTRON": None, "end_Protein_position": 74 }, "query_4": { "start_EXON": None, "start_INTRON": "1/2", "start_Protein_position": 54, "end_EXON": None, "end_INTRON": "2/2", "end_Protein_position": 74 }, "query_5": { "start_EXON": "1/3", "start_INTRON": None, "start_Protein_position": 44, "end_EXON": None, "end_INTRON": "2/2", "end_Protein_position": 74 }, "query_6": { "start_EXON": "1/3", "start_INTRON": None, "start_Protein_position": 1, "end_EXON": "2/3", "end_INTRON": None, "end_Protein_position": 71 }, "query_7": { "start_EXON": "1/3", "start_INTRON": None, "start_Protein_position": 38, "end_EXON": "2/3", "end_INTRON": None, "end_Protein_position": 71 }, "query_8": { "start_EXON": "1/3", "start_INTRON": None, "start_Protein_position": 1, "end_EXON": None, "end_INTRON": "2/2", "end_Protein_position": 74 }, "query_9": { "start_EXON": None, "start_INTRON": "1/2", "start_Protein_position": 54, "end_EXON": None, "end_INTRON": "2/2", "end_Protein_position": 74 } } for query_name, query_res in expected.items(): for key, val in { "SYMBOL": "gene_1", "Gene": "g_1", "Feature": "tr_1", "Feature_type": "Transcript", "STRAND": "-1" }.items(): query_res[key] = val # Apply reverse strand for exon in transcrit_1.children: exon.strand = "-" for cds in protein_1.children: cds.strand = "-" transcrit_1.sortChildren() protein_1.sortChildren() # Asert for curr_query in queries: annotations = getTranscriptsAnnot(curr_query, [transcrit_1]) self.assertEqual([expected[curr_query.name]], annotations)
def testGetTranscriptsAnnot_withoutUTR_oneExon(self): exon_1 = Exon(91, 150, "+", "chr1", "exon_2") cds_1 = CDS(91, 150, "+", "chr1", "cds_1") gene_1 = Gene(10, 350, None, "chr1", "gene_1", {"id": "g_1"}) transcrit_1 = Transcript(None, None, None, "chr1", "transcrit_1", {"id": "tr_1"}, parent=gene_1, children=[exon_1]) protein_1 = Protein(None, None, None, "chr1", "protein_2", children=[cds_1], transcript=transcrit_1) queries = [ Region(80, 160, None, "chr1", "query_1", {"desc": "starts before exon_1 ; ends after exon_1."}), Region( 91, 150, None, "chr1", "query_2", {"desc": "starts at start of exon_1 ; ends at end of exon_1." }), Region(100, 110, None, "chr1", "query_3", {"desc": "starts in exon_1 ; ends in exon_1."}), Region(80, 100, None, "chr1", "query_4", {"desc": "starts before exon_1 ; ends in exon_1."}), Region(110, 200, None, "chr1", "query_5", {"desc": "starts in exon_1 ; ends after exon_1."}), ] # Expected forward 1 exon expected = { "query_1": { "start_EXON": "1/1", "start_INTRON": None, "start_Protein_position": 1, "end_EXON": "1/1", "end_INTRON": None, "end_Protein_position": 20 }, "query_2": { "start_EXON": "1/1", "start_INTRON": None, "start_Protein_position": 1, "end_EXON": "1/1", "end_INTRON": None, "end_Protein_position": 20 }, "query_3": { "start_EXON": "1/1", "start_INTRON": None, "start_Protein_position": 4, "end_EXON": "1/1", "end_INTRON": None, "end_Protein_position": 7 }, "query_4": { "start_EXON": "1/1", "start_INTRON": None, "start_Protein_position": 1, "end_EXON": "1/1", "end_INTRON": None, "end_Protein_position": 4 }, "query_5": { "start_EXON": "1/1", "start_INTRON": None, "start_Protein_position": 7, "end_EXON": "1/1", "end_INTRON": None, "end_Protein_position": 20 }, } for query_name, query_res in expected.items(): for key, val in { "SYMBOL": "gene_1", "Gene": "g_1", "Feature": "tr_1", "Feature_type": "Transcript", "STRAND": "1" }.items(): query_res[key] = val # Apply forward strand for exon in transcrit_1.children: exon.strand = "+" for cds in protein_1.children: cds.strand = "+" transcrit_1.sortChildren() protein_1.sortChildren() # Asert for curr_query in queries: annotations = getTranscriptsAnnot(curr_query, [transcrit_1]) self.assertEqual([expected[curr_query.name]], annotations) # Expected reverse 1 exon expected = { "query_1": { "start_EXON": "1/1", "start_INTRON": None, "start_Protein_position": 1, "end_EXON": "1/1", "end_INTRON": None, "end_Protein_position": 20 }, "query_2": { "start_EXON": "1/1", "start_INTRON": None, "start_Protein_position": 1, "end_EXON": "1/1", "end_INTRON": None, "end_Protein_position": 20 }, "query_3": { "start_EXON": "1/1", "start_INTRON": None, "start_Protein_position": 14, "end_EXON": "1/1", "end_INTRON": None, "end_Protein_position": 17 }, "query_4": { "start_EXON": "1/1", "start_INTRON": None, "start_Protein_position": 17, "end_EXON": "1/1", "end_INTRON": None, "end_Protein_position": 20 }, "query_5": { "start_EXON": "1/1", "start_INTRON": None, "start_Protein_position": 1, "end_EXON": "1/1", "end_INTRON": None, "end_Protein_position": 14 }, } for query_name, query_res in expected.items(): for key, val in { "SYMBOL": "gene_1", "Gene": "g_1", "Feature": "tr_1", "Feature_type": "Transcript", "STRAND": "-1" }.items(): query_res[key] = val # Apply reverse strand for exon in transcrit_1.children: exon.strand = "-" for cds in protein_1.children: cds.strand = "-" transcrit_1.sortChildren() protein_1.sortChildren() # Asert for curr_query in queries: annotations = getTranscriptsAnnot(curr_query, [transcrit_1]) self.assertEqual([expected[curr_query.name]], annotations)
def setUp(self): tmp_folder = tempfile.gettempdir() unique_id = str(uuid.uuid1()) # Temporary files self.tmp_ensembl_in_gtf = os.path.join(tmp_folder, unique_id + "_ensembl_in.gtf") self.tmp_ensembl_out_gtf = os.path.join(tmp_folder, unique_id + "_ensembl_out.gtf") self.tmp_ncbi_in_gtf = os.path.join(tmp_folder, unique_id + "_ncbi_in.gtf") self.tmp_ncbi_out_gtf = os.path.join(tmp_folder, unique_id + "_ncbi_out.gtf") # Ensembl GTF self.ensembl_expected = [ Gene(54770583, 54771134, "+", "6", "KRASP1", { "id": "ENSG00000220635" }, None, [ Transcript( 54770583, 54771134, "+", "6", "KRASP1-201", {"id": "ENST00000407852"}, None, [Exon(54770583, 54771134, "+", "6", "ENST00000407852_e1")]) ]), Gene( 25204789, 25250936, "-", "12", "KRAS", {"id": "ENSG00000133703"}, None, [ Transcript( 25204789, 25250931, "-", "12", "KRAS-202", {"id": "ENST00000311936"}, None, [ Exon(25250751, 25250931, "-", "12", "ENST00000311936_e1"), Exon(25245274, 25245395, "-", "12", "ENST00000311936_e2"), Exon(25227234, 25227412, "-", "12", "ENST00000311936_e3"), Exon(25225614, 25225773, "-", "12", "ENST00000311936_e5"), Exon(25204789, 25209911, "-", "12", "ENST00000311936_e6") ], [ Protein(25209798, 25245384, "-", "12", None, None, None, [ CDS(25245274, 25245384, "-", "12", ""), CDS(25227234, 25227412, "-", "12", ""), CDS(25225614, 25225773, "-", "12", ""), CDS(25209798, 25209911, "-", "12", "") ]) ]), Transcript( 25209168, 25250936, "-", "12", "KRAS-204", {"id": "ENST00000557334"}, None, [ Exon(25250751, 25250936, "-", "12", "ENST00000557334_e1"), Exon(25245274, 25245395, "-", "12", "ENST00000557334_e2"), Exon(25209168, 25209911, "-", "12", "ENST00000557334_e3") ], [ Protein(25209798, 25245384, "-", "12", None, None, None, [ CDS(25245274, 25245384, "-", "12", ""), CDS(25209798, 25209911, "-", "12", "") ]) ]), Transcript( 25209431, 25250803, "-", "12", "KRAS-201", {"id": "ENST00000256078"}, None, [ Exon(25250751, 25250803, "-", "12", "ENST00000256078_e1"), Exon(25245274, 25245395, "-", "12", "ENST00000256078_e2"), Exon(25227234, 25227412, "-", "12", "ENST00000256078_e3"), Exon(25225614, 25225773, "-", "12", "ENST00000256078_e4"), Exon(25215437, 25215560, "-", "12", "ENST00000256078_e5"), Exon(25209431, 25209911, "-", "12", "ENST00000256078_e6") ], [ Protein(25215444, 25245384, "-", "12", None, None, None, [ CDS(25245274, 25245384, "-", "12", ""), CDS(25227234, 25227412, "-", "12", ""), CDS(25225614, 25225773, "-", "12", ""), CDS(25215444, 25215560, "-", "12", "") ]) ]), Transcript( 25233819, 25250929, "-", "12", "KRAS-203", {"id": "ENST00000556131"}, None, [ Exon(25250764, 25250929, "-", "12", "ENST00000556131_e1"), Exon(25245274, 25245395, "-", "12", "ENST00000556131_e2"), Exon(25233819, 25235226, "-", "12", "ENST00000556131_e3") ], [ Protein(25235209, 25245384, "-", "12", None, None, None, [ CDS(25245274, 25245384, "-", "12", ""), CDS(25235209, 25235226, "-", "12", "") ]) ]) ]) ] with open(self.tmp_ensembl_in_gtf, "w") as FH_gtf: FH_gtf.write("""#!genome-build GRCh38.p12 #!genome-version GRCh38 #!genome-date 2013-12 #!genome-build-accession NCBI:GCA_000001405.27 #!genebuild-last-updated 2018-07 6 havana gene 54770583 54771134 . + . gene_id \"ENSG00000220635\"; gene_version \"2\"; gene_name \"KRASP1\"; gene_source \"havana\"; gene_biotype \"processed_pseudogene\"; 6 havana transcript 54770583 54771134 . + . gene_id \"ENSG00000220635\"; gene_version \"2\"; transcript_id \"ENST00000407852\"; transcript_version \"2\"; gene_name \"KRASP1\"; gene_source \"havana\"; gene_biotype \"processed_pseudogene\"; transcript_name \"KRASP1-201\"; transcript_source \"havana\"; transcript_biotype \"processed_pseudogene\"; tag \"basic\"; transcript_support_level \"NA\"; 6 havana exon 54770583 54771134 . + . gene_id \"ENSG00000220635\"; gene_version \"2\"; transcript_id \"ENST00000407852\"; transcript_version \"2\"; exon_number \"1\"; gene_name \"KRASP1\"; gene_source \"havana\"; gene_biotype \"processed_pseudogene\"; transcript_name \"KRASP1-201\"; transcript_source \"havana\"; transcript_biotype \"processed_pseudogene\"; exon_id \"ENSE00001550689\"; exon_version \"2\"; tag \"basic\"; transcript_support_level \"NA\"; 12 ensembl_havana gene 25204789 25250936 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; 12 ensembl_havana transcript 25204789 25250931 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000311936\"; transcript_version \"7\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-202\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8702\"; tag \"basic\"; transcript_support_level \"1\"; 12 ensembl_havana exon 25250751 25250931 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000311936\"; transcript_version \"7\"; exon_number \"1\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-202\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8702\"; exon_id \"ENSE00001189804\"; exon_version \"4\"; tag \"basic\"; transcript_support_level \"1\"; 12 ensembl_havana exon 25245274 25245395 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000311936\"; transcript_version \"7\"; exon_number \"2\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-202\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8702\"; exon_id \"ENSE00000936617\"; exon_version \"1\"; tag \"basic\"; transcript_support_level \"1\"; 12 ensembl_havana CDS 25245274 25245384 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000311936\"; transcript_version \"7\"; exon_number \"2\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-202\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8702\"; protein_id \"ENSP00000308495\"; protein_version \"3\"; tag \"basic\"; transcript_support_level \"1\"; 12 ensembl_havana start_codon 25245382 25245384 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000311936\"; transcript_version \"7\"; exon_number \"2\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-202\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8702\"; tag \"basic\"; transcript_support_level \"1\"; 12 ensembl_havana exon 25227234 25227412 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000311936\"; transcript_version \"7\"; exon_number \"3\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-202\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8702\"; exon_id \"ENSE00001719809\"; exon_version \"1\"; tag \"basic\"; transcript_support_level \"1\"; 12 ensembl_havana CDS 25227234 25227412 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000311936\"; transcript_version \"7\"; exon_number \"3\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-202\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8702\"; protein_id \"ENSP00000308495\"; protein_version \"3\"; tag \"basic\"; transcript_support_level \"1\"; 12 ensembl_havana exon 25225614 25225773 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000311936\"; transcript_version \"7\"; exon_number \"4\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-202\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8702\"; exon_id \"ENSE00001644818\"; exon_version \"1\"; tag \"basic\"; transcript_support_level \"1\"; 12 ensembl_havana CDS 25225614 25225773 . - 1 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000311936\"; transcript_version \"7\"; exon_number \"4\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-202\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8702\"; protein_id \"ENSP00000308495\"; protein_version \"3\"; tag \"basic\"; transcript_support_level \"1\"; 12 ensembl_havana exon 25204789 25209911 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000311936\"; transcript_version \"7\"; exon_number \"5\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-202\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8702\"; exon_id \"ENSE00002456976\"; exon_version \"1\"; tag \"basic\"; transcript_support_level \"1\"; 12 ensembl_havana CDS 25209798 25209911 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000311936\"; transcript_version \"7\"; exon_number \"5\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-202\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8702\"; protein_id \"ENSP00000308495\"; protein_version \"3\"; tag \"basic\"; transcript_support_level \"1\"; 12 ensembl_havana stop_codon 25209795 25209797 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000311936\"; transcript_version \"7\"; exon_number \"5\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-202\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8702\"; tag \"basic\"; transcript_support_level \"1\"; 12 ensembl_havana five_prime_utr 25250751 25250931 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000311936\"; transcript_version \"7\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-202\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8702\"; tag \"basic\"; transcript_support_level \"1\"; 12 ensembl_havana five_prime_utr 25245385 25245395 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000311936\"; transcript_version \"7\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-202\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8702\"; tag \"basic\"; transcript_support_level \"1\"; 12 ensembl_havana three_prime_utr 25204789 25209794 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000311936\"; transcript_version \"7\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-202\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8702\"; tag \"basic\"; transcript_support_level \"1\"; 12 havana transcript 25209168 25250936 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000557334\"; transcript_version \"5\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-204\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; tag \"basic\"; transcript_support_level \"5\"; 12 havana exon 25250751 25250936 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000557334\"; transcript_version \"5\"; exon_number \"1\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-204\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; exon_id \"ENSE00002446502\"; exon_version \"1\"; tag \"basic\"; transcript_support_level \"5\"; 12 havana exon 25245274 25245395 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000557334\"; transcript_version \"5\"; exon_number \"2\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-204\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; exon_id \"ENSE00000936617\"; exon_version \"1\"; tag \"basic\"; transcript_support_level \"5\"; 12 havana CDS 25245274 25245384 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000557334\"; transcript_version \"5\"; exon_number \"2\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-204\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; protein_id \"ENSP00000452512\"; protein_version \"1\"; tag \"basic\"; transcript_support_level \"5\"; 12 havana start_codon 25245382 25245384 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000557334\"; transcript_version \"5\"; exon_number \"2\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-204\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; tag \"basic\"; transcript_support_level \"5\"; 12 havana exon 25209168 25209911 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000557334\"; transcript_version \"5\"; exon_number \"3\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-204\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; exon_id \"ENSE00002464674\"; exon_version \"1\"; tag \"basic\"; transcript_support_level \"5\"; 12 havana CDS 25209798 25209911 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000557334\"; transcript_version \"5\"; exon_number \"3\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-204\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; protein_id \"ENSP00000452512\"; protein_version \"1\"; tag \"basic\"; transcript_support_level \"5\"; 12 havana stop_codon 25209795 25209797 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000557334\"; transcript_version \"5\"; exon_number \"3\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-204\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; tag \"basic\"; transcript_support_level \"5\"; 12 havana five_prime_utr 25250751 25250936 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000557334\"; transcript_version \"5\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-204\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; tag \"basic\"; transcript_support_level \"5\"; 12 havana five_prime_utr 25245385 25245395 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000557334\"; transcript_version \"5\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-204\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; tag \"basic\"; transcript_support_level \"5\"; 12 havana three_prime_utr 25209168 25209794 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000557334\"; transcript_version \"5\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-204\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; tag \"basic\"; transcript_support_level \"5\"; 12 ensembl_havana transcript 25209431 25250803 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; tag \"basic\"; transcript_support_level \"1\"; 12 ensembl_havana exon 25250751 25250803 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; exon_number \"1\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; exon_id \"ENSE00002513959\"; exon_version \"1\"; tag \"basic\"; transcript_support_level \"1\"; 12 ensembl_havana exon 25245274 25245395 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; exon_number \"2\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; exon_id \"ENSE00000936617\"; exon_version \"1\"; tag \"basic\"; transcript_support_level \"1\"; 12 ensembl_havana CDS 25245274 25245384 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; exon_number \"2\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; protein_id \"ENSP00000256078\"; protein_version \"4\"; tag \"basic\"; transcript_support_level \"1\"; 12 ensembl_havana start_codon 25245382 25245384 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; exon_number \"2\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; tag \"basic\"; transcript_support_level \"1\"; 12 ensembl_havana exon 25227234 25227412 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; exon_number \"3\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; exon_id \"ENSE00001719809\"; exon_version \"1\"; tag \"basic\"; transcript_support_level \"1\"; 12 ensembl_havana CDS 25227234 25227412 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; exon_number \"3\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; protein_id \"ENSP00000256078\"; protein_version \"4\"; tag \"basic\"; transcript_support_level \"1\"; 12 ensembl_havana exon 25225614 25225773 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; exon_number \"4\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; exon_id \"ENSE00001644818\"; exon_version \"1\"; tag \"basic\"; transcript_support_level \"1\"; 12 ensembl_havana CDS 25225614 25225773 . - 1 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; exon_number \"4\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; protein_id \"ENSP00000256078\"; protein_version \"4\"; tag \"basic\"; transcript_support_level \"1\"; 12 ensembl_havana exon 25215437 25215560 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; exon_number \"5\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; exon_id \"ENSE00001189807\"; exon_version \"5\"; tag \"basic\"; transcript_support_level \"1\"; 12 ensembl_havana CDS 25215444 25215560 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; exon_number \"5\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; protein_id \"ENSP00000256078\"; protein_version \"4\"; tag \"basic\"; transcript_support_level \"1\"; 12 ensembl_havana stop_codon 25215441 25215443 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; exon_number \"5\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; tag \"basic\"; transcript_support_level \"1\"; 12 ensembl_havana exon 25209431 25209911 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; exon_number \"6\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; exon_id \"ENSE00002477035\"; exon_version \"1\"; tag \"basic\"; transcript_support_level \"1\"; 12 ensembl_havana five_prime_utr 25250751 25250803 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; tag \"basic\"; transcript_support_level \"1\"; 12 ensembl_havana five_prime_utr 25245385 25245395 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; tag \"basic\"; transcript_support_level \"1\"; 12 ensembl_havana three_prime_utr 25215437 25215440 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; tag \"basic\"; transcript_support_level \"1\"; 12 ensembl_havana three_prime_utr 25209431 25209911 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000256078\"; transcript_version \"8\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-201\"; transcript_source \"ensembl_havana\"; transcript_biotype \"protein_coding\"; tag \"CCDS\"; ccds_id \"CCDS8703\"; tag \"basic\"; transcript_support_level \"1\"; 12 havana transcript 25233819 25250929 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000556131\"; transcript_version \"1\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-203\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; tag \"basic\"; transcript_support_level \"1\"; 12 havana exon 25250764 25250929 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000556131\"; transcript_version \"1\"; exon_number \"1\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-203\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; exon_id \"ENSE00002530521\"; exon_version \"1\"; tag \"basic\"; transcript_support_level \"1\"; 12 havana exon 25245274 25245395 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000556131\"; transcript_version \"1\"; exon_number \"2\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-203\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; exon_id \"ENSE00000936617\"; exon_version \"1\"; tag \"basic\"; transcript_support_level \"1\"; 12 havana CDS 25245274 25245384 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000556131\"; transcript_version \"1\"; exon_number \"2\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-203\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; protein_id \"ENSP00000451856\"; protein_version \"1\"; tag \"basic\"; transcript_support_level \"1\"; 12 havana start_codon 25245382 25245384 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000556131\"; transcript_version \"1\"; exon_number \"2\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-203\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; tag \"basic\"; transcript_support_level \"1\"; 12 havana exon 25233819 25235226 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000556131\"; transcript_version \"1\"; exon_number \"3\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-203\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; exon_id \"ENSE00002478081\"; exon_version \"1\"; tag \"basic\"; transcript_support_level \"1\"; 12 havana CDS 25235209 25235226 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000556131\"; transcript_version \"1\"; exon_number \"3\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-203\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; protein_id \"ENSP00000451856\"; protein_version \"1\"; tag \"basic\"; transcript_support_level \"1\"; 12 havana stop_codon 25235206 25235208 . - 0 gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000556131\"; transcript_version \"1\"; exon_number \"3\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-203\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; tag \"basic\"; transcript_support_level \"1\"; 12 havana five_prime_utr 25250764 25250929 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000556131\"; transcript_version \"1\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-203\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; tag \"basic\"; transcript_support_level \"1\"; 12 havana five_prime_utr 25245385 25245395 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000556131\"; transcript_version \"1\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-203\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; tag \"basic; other\"; transcript_support_level \"1\"; 12 havana three_prime_utr 25233819 25235205 . - . gene_id \"ENSG00000133703\"; gene_version \"11\"; transcript_id \"ENST00000556131\"; transcript_version \"1\"; gene_name \"KRAS\"; gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\"; transcript_name \"KRAS-203\"; transcript_source \"havana\"; transcript_biotype \"protein_coding\"; tag \"basic;\"; transcript_support_level \"1\";""" ) # NCBI GTF self.ncbi_expected = [ Gene(54635272, 54640529, "+", "6", "KRASP1", {"id": "3844"}, None, [ Transcript( 54635272, 54640529, "+", "6", "gene14201", {"id": "gene14201"}, None, [Exon(54635272, 54640529, "+", "6", "gene14201_e1")]) ]), Gene(25357723, 25403865, "-", "12", "KRAS", {"id": "3845"}, None, [ Transcript( 25357723, 25403865, "-", "12", "rna36549", {"id": "rna36549"}, None, [ Exon(25357723, 25362845, "-", "12", "rna36549_e1"), Exon(25378548, 25378707, "-", "12", "rna36549_e2"), Exon(25380168, 25380346, "-", "12", "rna36549_e3"), Exon(25398208, 25398329, "-", "12", "rna36549_e5"), Exon(25403685, 25403865, "-", "12", "rna36549_e6") ], [ Protein(25362729, 25398318, "-", "12", None, None, None, [ CDS(25362729, 25362845, "-", "12", ""), CDS(25378548, 25378707, "-", "12", ""), CDS(25380168, 25380346, "-", "12", ""), CDS(25398208, 25398318, "-", "12", "") ]) ]), Transcript(25357723, 25403865, "-", "12", "rna36550", { "id": "rna36550" }, None, [ Exon(25357723, 25362845, "-", "12", "rna36550_e1"), Exon(25368371, 25368494, "-", "12", "rna36550_e2"), Exon(25378548, 25378707, "-", "12", "rna36550_e3"), Exon(25380168, 25380346, "-", "12", "rna36550_e4"), Exon(25398208, 25398329, "-", "12", "rna36550_e5"), Exon(25403685, 25403865, "-", "12", "rna36550_e6") ], [ Protein(25368375, 25398318, "-", "12", None, None, None, [ CDS(25368375, 25368494, "-", "12", ""), CDS(25378548, 25378707, "-", "12", ""), CDS(25380168, 25380346, "-", "12", ""), CDS(25398208, 25398318, "-", "12", ""), ]) ]) ]), Gene(2527306, 2529079, "+", "X", "CD99P1", {"id": "401577"}, None, [ Transcript( 2527306, 2529079, "+", "X", "rna58916", {"id": "rna58916"}, None, [ Exon(2527306, 2527522, "+", "X", "rna58916_e1"), Exon(2529037, 2529079, "+", "X", "rna58916_e2") ]) ]), Gene(2477306, 2479079, "+", "Y", "CD99P1", {"id": "401577"}, None, [ Transcript( 2477306, 2479079, "+", "Y", "rna61353", {"id": "rna61353"}, None, [ Exon(2477306, 2477522, "+", "Y", "rna61353_e1"), Exon(2479037, 2479079, "+", "Y", "rna61353_e2") ]) ]) ] with open(self.tmp_ncbi_in_gtf, "w") as FH_gtf: FH_gtf.write( """6 Curated Genomic exon 54635272 54640529 . + . transcript_id \"gene14201\"; gene_id \"3844\"; gene_name \"KRASP1\"; 12 BestRefSeq exon 25357723 25362845 . - . transcript_id \"rna36549\"; gene_id \"3845\"; gene_name \"KRAS\"; 12 BestRefSeq exon 25378548 25378707 . - . transcript_id \"rna36549\"; gene_id \"3845\"; gene_name \"KRAS\"; 12 BestRefSeq exon 25380168 25380346 . - . transcript_id \"rna36549\"; gene_id \"3845\"; gene_name \"KRAS\"; 12 BestRefSeq exon 25398208 25398329 . - . transcript_id \"rna36549\"; gene_id \"3845\"; gene_name \"KRAS\"; 12 BestRefSeq exon 25403685 25403865 . - . transcript_id \"rna36549\"; gene_id \"3845\"; gene_name \"KRAS\"; 12 BestRefSeq CDS 25362729 25362845 . - 0 transcript_id \"rna36549\"; gene_id \"3845\"; gene_name \"KRAS\"; 12 BestRefSeq CDS 25378548 25378707 . - 1 transcript_id \"rna36549\"; gene_id \"3845\"; gene_name \"KRAS\"; 12 BestRefSeq CDS 25380168 25380346 . - 0 transcript_id \"rna36549\"; gene_id \"3845\"; gene_name \"KRAS\"; 12 BestRefSeq CDS 25398208 25398318 . - 0 transcript_id \"rna36549\"; gene_id \"3845\"; gene_name \"KRAS\"; 12 BestRefSeq exon 25357723 25362845 . - . transcript_id \"rna36550\"; gene_id \"3845\"; gene_name \"KRAS\"; 12 BestRefSeq exon 25368371 25368494 . - . transcript_id \"rna36550\"; gene_id \"3845\"; gene_name \"KRAS\"; 12 BestRefSeq exon 25378548 25378707 . - . transcript_id \"rna36550\"; gene_id \"3845\"; gene_name \"KRAS\"; 12 BestRefSeq exon 25380168 25380346 . - . transcript_id \"rna36550\"; gene_id \"3845\"; gene_name \"KRAS\"; 12 BestRefSeq exon 25398208 25398329 . - . transcript_id \"rna36550\"; gene_id \"3845\"; gene_name \"KRAS\"; 12 BestRefSeq exon 25403685 25403865 . - . transcript_id \"rna36550\"; gene_id \"3845\"; gene_name \"KRAS\"; 12 BestRefSeq CDS 25368375 25368494 . - 0 transcript_id \"rna36550\"; gene_id \"3845\"; gene_name \"KRAS\"; 12 BestRefSeq CDS 25378548 25378707 . - 1 transcript_id \"rna36550\"; gene_id \"3845\"; gene_name \"KRAS\"; 12 BestRefSeq CDS 25380168 25380346 . - 0 transcript_id \"rna36550\"; gene_id \"3845\"; gene_name \"KRAS\"; 12 BestRefSeq CDS 25398208 25398318 . - 0 transcript_id \"rna36550\"; gene_id \"3845\"; gene_name \"KRAS\"; X BestRefSeq exon 2527306 2527522 . + . transcript_id \"rna58916\"; gene_id \"401577\"; gene_name \"CD99P1\"; X BestRefSeq exon 2529037 2529079 . + . transcript_id \"rna58916\"; gene_id \"401577\"; gene_name \"CD99P1\"; Y BestRefSeq exon 2477306 2477522 . + . transcript_id \"rna61353\"; gene_id \"401577\"; gene_name \"CD99P1\"; Y BestRefSeq exon 2479037 2479079 . + . transcript_id \"rna61353\"; gene_id \"401577\"; gene_name \"CD99P1\";""" )