From 36d33ac2c366c0f0702ab50fdcab37261add7b9c Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Tue, 25 Oct 2022 09:44:46 +0200
Subject: [PATCH] Option to consider features all-exonic.
This is used for spike-ins, whose gtf file does not contain "exon"
features.
---
libhts/__init__.py | 4 ++--
libhts/libhts.py | 14 ++++++++++++--
2 files changed, 14 insertions(+), 4 deletions(-)
diff --git a/libhts/__init__.py b/libhts/__init__.py
index 3ad8378..1315de5 100644
--- a/libhts/__init__.py
+++ b/libhts/__init__.py
@@ -1,8 +1,8 @@
from subprocess import check_output
-__copyright__ = "Copyright (C) 2020-2021 Blaise Li"
+__copyright__ = "Copyright (C) 2020-2022 Blaise Li"
__licence__ = "GNU GPLv3"
-__version__ = 0.6
+__version__ = 0.7
BEDTOOLS_VERSION = check_output(
["bedtools", "--version"]).decode("utf-8").strip().split()[-1]
diff --git a/libhts/libhts.py b/libhts/libhts.py
index a7eff6e..8b9c621 100644
--- a/libhts/libhts.py
+++ b/libhts/libhts.py
@@ -141,10 +141,20 @@ class Gene():
self.exons, OVERLAP).nodes()))
-def gtf_2_genes_exon_lengths(gtf_filename):
- """Returns a pandas DataFrame where union exon lengths are associated to gene IDs."""
+def gtf_2_genes_exon_lengths(gtf_filename, direct_len=False):
+ """
+ Return a pandas DataFrame where union exon lengths are associated to gene IDs.
+
+ If *direct_len* is set to `True`, features in the gtf file are assumed to be
+ "all exonic" and their length is taken directly without further controls.
+ This can be used for instance when dealing with spike-ins.
+ """
gtf_file = open(gtf_filename, "r")
gtf = BedTool(gtf_file)
+ if direct_len:
+ return pd.DataFrame(pd.Series(
+ {feature.attrs["gene_id"] : len(feature) for feature in gtf.features()},
+ name=("union_exon_len")).rename_axis("gene"))
genes = {}
for feature in gtf.features():
feat_type = feature[2]
--
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