From 4462494b5b6cfe45325287ea27a35e9993d39f12 Mon Sep 17 00:00:00 2001
From: Mia Croiset <mia.croiset@ens-lyon.fr>
Date: Mon, 22 Jan 2024 14:13:29 +0100
Subject: [PATCH] test change command cutsite
---
bin/hicstuff_build_matrix.py | 18 +++++++++++-------
1 file changed, 11 insertions(+), 7 deletions(-)
diff --git a/bin/hicstuff_build_matrix.py b/bin/hicstuff_build_matrix.py
index bd68ee0..194a9d3 100755
--- a/bin/hicstuff_build_matrix.py
+++ b/bin/hicstuff_build_matrix.py
@@ -63,13 +63,17 @@ def pairs2matrix(
)
pre_mat_file = mat_file + ".pre.pairs"
- hio.sort_pairs(
- pairs_file,
- pre_mat_file,
- keys=["frag1", "frag2"],
- threads=threads,
- tmp_dir=tmp_dir,
- )
+ # hio.sort_pairs(
+ # pairs_file,
+ # pre_mat_file,
+ # keys=["frag1", "frag2"],
+ # threads=threads,
+ # tmp_dir=tmp_dir,
+ # )
+
+ cmd = 'grep -v ^# %s | sort -S 2G -k8,8n -k9,9n --parallel=1' % pairs_file
+ os.system(cmd '>>' prem_mat_file)
+
header_size = len(hio.get_pairs_header(pre_mat_file))
with open(pre_mat_file, "r") as pairs, open(mat_file, "w") as mat:
# Skip header lines
--
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