From a88295f69c49c9e71567c8e6be1b06832450cafe Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Fri, 5 Feb 2021 15:31:12 +0100
Subject: [PATCH] src/find_interaction_cluster/clip_figures/__main__.py: add a
parameter cell line
---
src/find_interaction_cluster/clip_figures/__main__.py | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/src/find_interaction_cluster/clip_figures/__main__.py b/src/find_interaction_cluster/clip_figures/__main__.py
index 5c07cf85..5891a4d2 100644
--- a/src/find_interaction_cluster/clip_figures/__main__.py
+++ b/src/find_interaction_cluster/clip_figures/__main__.py
@@ -16,6 +16,7 @@ from .clip_analyser import clip_folder_analysis
def clip_analysis(clip_folder: str, weight: int = -1,
global_weight: int = -1, same_gene: bool = True,
inflation: float = 1.5,
+ cell_line: str = "ALL",
feature: str = "exon",
project: str = "GSM1018963_GSM1018964",
test_type: str = "permutation", iteration: int = 10000,
@@ -34,6 +35,8 @@ def clip_analysis(clip_folder: str, weight: int = -1,
:param same_gene: Say if we consider as co-localised, exons within the \
same gene (True) or not (False) (default False)
:param inflation: The inflation parameter (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 feature: The feature we want to analyse (default 'exon')
:param clip_folder: A folder containing clip file
:param test_type: The kind of test to perform for frequency analysis. \
@@ -59,8 +62,8 @@ def clip_analysis(clip_folder: str, weight: int = -1,
if not clip_folder.is_dir():
raise NotADirectoryError(f"{clip_folder} is not an existing directory")
clip_folder_analysis(clip_folder, project, weight, global_weight,
- same_gene, inflation, feature, test_type, iteration,
- display_size, community_file, sl_reg, ps,
+ same_gene, inflation, cell_line, feature, test_type,
+ iteration, display_size, community_file, sl_reg, ps,
logging_level)
--
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