src/download_encode_eclip/merge_eclip.py: add a parameter level in...

src/download_encode_eclip/merge_eclip.py: add a parameter level in create_merged_files function to filter within genes (without first and last exons) or within exons (extended by 200 nt at each side)

src/download_encode_eclip/merge_eclip.py

@@ -127,17 +127,18 @@ def group_files(mfiles: List[Path], target: str) -> Dict[str, List[Path]]:
     return d
 
 
-def merge_files(dfiles: Dict[str, List[Path]], target: str) -> None:
+def merge_files(dfiles: Dict[str, List[Path]], target: str, filter_bed: Path
+                ) -> None:
     """
     Merge the file together.
 
     :param dfiles: A dictionary that links each target to the files of interest
     :param target: The level used to group the files. (factor, replicate, cell)
+    :param filter_bed: bed used to filter the clip peaks
     :return: The merged bed file
     """
     outfolder = ConfigEncodeClip.merged_output / target
     outfolder.mkdir(parents=True, exist_ok=True)
-    gene_bed = ConfigEncodeClip.output_gene
     for k in dfiles:
         print(f"Working on {k}")
         tmp_out = outfolder / f"{k}_tmp.bed"
@@ -146,11 +147,11 @@ def merge_files(dfiles: Dict[str, List[Path]], target: str) -> None:
         list_file = " ".join(map(str, dfiles[k]))
         cmd = "zcat %s | awk 'BEGIN{FS=\"\\t\"}{if($5==1000){print $0}}' " \
               "> %s" % (list_file, tmp_out)
-        cmd2 = f"bedtools intersect -a {tmp_out} -b {gene_bed} -s " \
+        cmd2 = f"bedtools intersect -a {tmp_out} -b {filter_bed} -s " \
                f"| sort -k1,1 -k2,2n > {tmp_out2}"
         cmd3 = f"bedtools merge -i {tmp_out2} -d -1 -s -c 4,5,6 " \
-               f"-o collapse,mean,distinct | cut -f1-3,5-7 | sed 's/^chr//g' " \
-               f"| gzip -c > {res_out}"
+               f"-o collapse,mean,distinct | cut -f1-3,5-7 | " \
+               f"sed 's/^chr//g' | gzip -c > {res_out}"
         sp.check_output(cmd, shell=True)
         sp.check_output(cmd2, shell=True)
         sp.check_output(cmd3, shell=True)
@@ -161,18 +162,20 @@ def merge_files(dfiles: Dict[str, List[Path]], target: str) -> None:
 @lp.parse(assay=["eCLIP", "iCLIP", "RIP-chip", "RIP-seq"],
           target=["factor", "replicate", "cell"])
 def create_merged_files(assay: List[str] = ("eCLIP", "iCLIP"),
-                        target: str = "factor"):
+                        target: str = "factor", level: str = "exon"):
     """
 
     :param assay: The kind of assay of interest(default ['eCLIP', 'iCLIP']
     :param target: The level used to group the files. (factor, replicate, \
     cell) (default 'factor').
+    :param level: 'gene' to create a bed file without first and last exons \
+    'exon' to create a bed file of extended exon (200nt at each size) \
+    without first and last exon (default exon)
     """
-    if not ConfigEncodeClip.output_gene.is_file():
-        create_gene_bed()
+    filter_bed = create_gene_bed(level)
     mfiles = load_clip_files(assay)
     dfiles = group_files(mfiles, target)
-    merge_files(dfiles, target)
+    merge_files(dfiles, target, filter_bed)
 
 
 if __name__ == "__main__":