From 59c9b619d924d6cfdd58f44d49101bb584f2f34c Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Fri, 5 Feb 2021 11:34:30 +0100
Subject: [PATCH] add a cell line parameter
---
src/nt_composition/__main__.py | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/src/nt_composition/__main__.py b/src/nt_composition/__main__.py
index a6c34da3..9c146ef6 100644
--- a/src/nt_composition/__main__.py
+++ b/src/nt_composition/__main__.py
@@ -22,6 +22,7 @@ def launcher(weight: int = 1, global_weight: int = 0, ft_type: str = 'nt',
same_gene: bool = False, compute_mean: bool = True,
iteration: int = 10000, kind: str = 'density',
community_size: int = -1, inflation: float = 1.5,
+ cell_line: str = "ALL",
inter_chr: bool = False,
level: str = "exon",
logging_level: str = "DISABLE"):
@@ -50,6 +51,8 @@ def launcher(weight: int = 1, global_weight: int = 0, ft_type: str = 'nt',
than community size. if community_size = -1. This option is deactivated.
:param inflation: The inflation parameter. This parameter is used only \
if community size is not -1. (default 1.5).
+ :param cell_line: Interactions are only selected from projects made on \
+ a specific cell line (ALL to disable this filter). (default ALL)
:param inter_chr: True to only get inter-chromosomal interactions \
False else (default: False)
:param level: The kind of feature to analyse (exon or gene)
@@ -60,7 +63,7 @@ def launcher(weight: int = 1, global_weight: int = 0, ft_type: str = 'nt',
community_size = None
if kind == "density":
create_all_frequency_figures(ConfigNt.cpu, weight, global_weight,
- ft_type, same_gene, inflation,
+ ft_type, same_gene, inflation, cell_line,
compute_mean, community_size, inter_chr,
level, logging_level)
else:
--
GitLab