diff --git a/jass/models/inittable.py b/jass/models/inittable.py index 7a2849dd59bec963d53866aab2f3754a72b40cf3..b6cde3dd69f879a63287ff392680a3cde58631c7 100644 --- a/jass/models/inittable.py +++ b/jass/models/inittable.py @@ -375,6 +375,7 @@ def add_gene_annotation( gene_start = [] gene_end = [] gene_direction = [] + gene_biotype = [] # lists containing exon data exon_id_label = [] @@ -414,6 +415,23 @@ def add_gene_annotation( decode_id_4 = decode_id_3[0].split("=") decode_id_5 = decode_id_4[1].split(":") gene_GeneID.append(decode_id_5[1]) + decode_id_6 = decode_id_1[5].split("=") + if decode_id_6[0] == "gene_biotype": + The_biotype = decode_id_6[1].rstrip('\r\n') + gene_biotype.append(The_biotype) + else: + decode_id_7 = decode_id_1[6].split("=") + if decode_id_7[0] == "gene_biotype": + The_biotype = decode_id_7[1].rstrip('\r\n') + gene_biotype.append(The_biotype) + else: + decode_id_8 = decode_id_1[7].split("=") + if decode_id_8[0] == "gene_biotype": + The_biotype = decode_id_8[1].rstrip('\r\n') + gene_biotype.append(The_biotype) + else: + The_biotype = "unknown" + gene_biotype.append(The_biotype) elif elements[2] == "exon": TMP__exon_chr.append(chr) @@ -447,6 +465,7 @@ def add_gene_annotation( "start": gene_start, "end": gene_end, "direction": gene_direction, + "biotype": gene_biotype, } ) df_exon = DataFrame(