From 492654cbb1c0abef06a39819f2687c75bf2662ea Mon Sep 17 00:00:00 2001
From: Cyril NERIN <cnerin@pasteur.fr>
Date: Tue, 27 Jul 2021 17:12:53 +0200
Subject: [PATCH] FEAT #83
---
jass/models/inittable.py | 19 +++++++++++++++++++
1 file changed, 19 insertions(+)
diff --git a/jass/models/inittable.py b/jass/models/inittable.py
index 7a2849dd..b6cde3dd 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(
--
GitLab