From 72caf926eae531af7df09b8ed7030d353cc9ffd6 Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Wed, 15 Jul 2020 15:44:44 +0200
Subject: [PATCH] src/nt_composition/__main__.py: addition of parameter
community_size to limit nt frequency analysis to only exons located in large
community of co-regulated exons. This parameter can be set to -1 for using
the old behavior
---
src/nt_composition/__main__.py | 8 +++++++-
1 file changed, 7 insertions(+), 1 deletion(-)
diff --git a/src/nt_composition/__main__.py b/src/nt_composition/__main__.py
index 3f931ee7..72e99bbc 100644
--- a/src/nt_composition/__main__.py
+++ b/src/nt_composition/__main__.py
@@ -21,6 +21,7 @@ import lazyparser as lp
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,
logging_level: str = "DISABLE"):
"""
Launch the creation of density file.
@@ -42,13 +43,18 @@ def launcher(weight: int = 1, global_weight: int = 0, ft_type: str = 'nt',
correlation figure between the feature frequency of an exon and the \
frequency of the same feature for other co-localized exons. 'distance' \
to check if the frequencies of co-localized exon are closer than \
- randomly expected. (default : 'density').
+ randomly expected. (default : 'density').*
+ :param community_size: consider only exons within communities bigger
+ than community size. if community_size = -1. This option is deactivated.
:param logging_level: The level of data to display (default 'DISABLE')
"""
get_interactions_number(weight, same_gene, logging_level)
+ if community_size == -1:
+ community_size = None
if kind == "density":
create_all_frequency_figures(ConfigNt.cpu, weight, global_weight,
ft_type, same_gene, compute_mean,
+ community_size,
logging_level)
else:
create_all_distance_figures(ConfigNt.cpu, weight, global_weight,
--
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