From 56cfa04d8e2cc980b36829069d9606d27646dc37 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Thu, 17 Dec 2020 17:42:23 +0100
Subject: [PATCH] Gene-list filtering in extract_annot_start.py.
Also have setup.py install the script.
---
README.md | 5 +++--
scripts/extract_annot_start.py | 10 ++++++++++
setup.py | 3 ++-
3 files changed, 15 insertions(+), 3 deletions(-)
diff --git a/README.md b/README.md
index 6b9334c..4ac7e5a 100644
--- a/README.md
+++ b/README.md
@@ -5,9 +5,10 @@ This Python package also installs some shell scripts:
* `sam2indexedbam.sh` (depends on samtools)
* `bam2bigwig.sh` (depends on bedops, python3, samtools, bedtools, niceload from parallel and bedGraphToBigWig from UCSC-tools)
-It also provides a Python script to transfer bigwig data from one region to another:
+It also provides some Python scripts.
-* `copypaste_bigwig_regions.py`
+* `copypaste_bigwig_regions.py` to transfer bigwig data from one region to another.
+* `extract_annot_start.py` to extract starting portions of bed records.
## Installing
diff --git a/scripts/extract_annot_start.py b/scripts/extract_annot_start.py
index 10b3483..2da9b6a 100755
--- a/scripts/extract_annot_start.py
+++ b/scripts/extract_annot_start.py
@@ -35,6 +35,11 @@ def main():
"-b", "--bedfile",
required=True,
help="Input bed file.")
+ parser.add_argument(
+ "-g", "--gene_list",
+ help="File containing a list of gene identifiers. "
+ "If provided, only annotations whose 4th column "
+ "matches one of these identifiers will be considered.")
parser.add_argument(
"-s", "--start_size",
type=int,
@@ -48,10 +53,15 @@ def main():
start_size = args.start_size
keep_short = args.keep_short
+ if args.gene_list:
+ with open(args.gene_list) as gene_list_fh:
+ gene_ids = set(line.strip() for line in gene_list_fh)
nb_too_short = 0
with open(args.bedfile) as bedfile:
for line in bedfile:
(chrom, start, end, name, score, strand) = line.strip().split("\t")
+ if gene_ids and name not in gene_ids:
+ continue
if int(end) - int(start) < start_size:
nb_too_short += 1
if keep_short:
diff --git a/setup.py b/setup.py
index 3b05700..e0abc75 100644
--- a/setup.py
+++ b/setup.py
@@ -34,7 +34,8 @@ setup(
packages=find_packages(),
scripts=[
"scripts/bam2bigwig.sh", "scripts/sam2indexedbam.sh",
- "scripts/copypaste_bigwig_regions.py"],
+ "scripts/copypaste_bigwig_regions.py",
+ "scripts/extract_annot_start.py"],
install_requires=[
#"libworkflows @ git+https://gitlab+deploy-token-31:isEzpsgbNf2sJMdUDy2g@gitlab.pasteur.fr/bli/libworkflows.git@744dd79b579577cb6e131653260d7990946be3ad#egg=libworkflows-0.1",
#"libworkflows @ git+https://gitlab+deploy-token-31:isEzpsgbNf2sJMdUDy2g@gitlab.pasteur.fr/bli/libworkflows.git#egg=libworkflows-0.1",
--
GitLab