src/bed_handler/filter_bed.py: add an option keep to recover every other genes...

src/bed_handler/filter_bed.py: add an option keep to recover every other genes not in the filter_file

src/bed_handler/filter_bed.py

@@ -30,7 +30,7 @@ def select_ft_of_interest(gene_file: Path) -> List[int]:
             gene_id for gene_id in gene_list]
 
 
-def filter_bed(bed_file: Path, gene_list: List[int], col_name: str
+def filter_bed(bed_file: Path, gene_list: List[int], col_name: str, keep: bool
                ) -> pd.DataFrame:
     """
     load a bed containing FasterDB gene and only recover the gene of \
@@ -40,21 +40,34 @@ def filter_bed(bed_file: Path, gene_list: List[int], col_name: str
     :param gene_list: a list of gene of interest
     :param col_name: The column in the bed file containing the valeus \
     stored in `gene_list`
+    :param keep: if true the everything inside the filter_file is kept \
+    otherwise it is dropped from the original bed file
     :return: The bed file bed containing only genes located in gene_list
 
-    >>> filter_bed(TestConfig.gene_bed, [1, 5, 9], "id")
+    >>> filter_bed(TestConfig.gene_bed, [1, 5, 9], "id", True)
        #ref     start       end  id     score strand
     0    18  28645943  28682388   1      DSC2      -
     4    13  45766989  45775176   5     KCTD4      -
     8    13  45967450  45992516   9  SLC25A30      -
+    >>> filter_bed(TestConfig.gene_bed, [1, 5, 9], "id", False)
+       #ref     start       end  id       score strand
+    1    18  28709190  28742819   2        DSC1      -
+    2    18  28898050  28937394   3        DSG1      +
+    3    18  28956739  28994869   4        DSG4      +
+    5    13  45911001  45915347   6        TPT1      -
+    6    18  48918411  49088839   7  AC011260.1      +
+    7    18  49866541  51062273   8         DCC      +
     """
     df = pd.read_csv(bed_file, sep="\t")
-    return df[df[col_name].isin(gene_list)]
+    if keep:
+        return df[df[col_name].isin(gene_list)]
+    return df[-df[col_name].isin(gene_list)]
 
 
 @lp.parse(bed_file="file", filter_file="file")
 def create_filtered_bed(bed_file: str, filter_file: str, col_name: str,
-                        outfile: str, output: str = str(OutputBed.output)):
+                        outfile: str, output: str = str(OutputBed.output),
+                        keep: str = 'y'):
     """
     Filter the bed_file given with --bed_file parameter to only keep the \
     rows containing the values stored in the file given with \
@@ -68,9 +81,12 @@ def create_filtered_bed(bed_file: str, filter_file: str, col_name: str,
     :param outfile: The name of the filtered ned file
     :param output: Folder where the filtered bam will be created (default \
     results/bed_file)
+    :param keep: if 'y' the everything inside the filter_file is kept \
+    otherwise it is dropped from the original bed file (default 'y')
     """
+    k = keep.lower() == 'y'
     ft_list = select_ft_of_interest(Path(filter_file))
-    df = filter_bed(Path(bed_file), ft_list, col_name)
+    df = filter_bed(Path(bed_file), ft_list, col_name, k)
     df.to_csv(Path(output) / outfile, sep="\t", index=False)