Merge branch 'master' of gitbio.ens-lyon.fr:LBMC/regards/chia-pet_network

src/figures_utils/config_figures.py

@@ -8,6 +8,51 @@ Description: Configuration class
 
 
 from pathlib import Path
+from typing import List
+from itertools import filterfalse
+from doctest import testmod
+import re
+
+
+def get_p(x: str):
+    """
+    return False if x contains 'Keep' True else
+
+    >>> get_p('Keep: GMX32, GSM78')
+    False
+    >>> get_p('Delete: Bou, foo, bar')
+    True
+    """
+    if "Keep" in x:
+        return False
+    else:
+        return True
+
+
+def get_good_project() -> List[str]:
+    """
+    Return only good ChIA-PET projects base on TAD co-localisation results
+
+    :return: The list of project to keep
+
+    >>> res = get_good_project()
+    >>> type(res)
+    <class 'list'>
+    >>> len(res) > 0
+    True
+    >>> "GSM1018963_GSM1018964" in res
+    True
+    >>> res[0:2]
+    ['GSM1018963_GSM1018964', 'GSM1018961_GSM1018962']
+    >>> pat = re.compile(r"[GSM0-9_]+")
+    >>> sum([re.findall(pat, c)[0] == c for c in res]) == len(res)
+    True
+    """
+
+    with Config.file_datasets_filtering.open('r') as f:
+        line = next(filterfalse(get_p, f)).replace("Keep: ", "").\
+            replace('\n', '')
+    return line.split(', ')
 
 
 class Config:
@@ -22,3 +67,7 @@ class Config:
     db_file = results / 'chia_pet_database.db'
     draw_number = 1000
     file_datasets_filtering = results / "projects_filtering.txt"
+
+
+if __name__ == "__main__":
+    testmod()
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