Merge pull request #19 from Marmzy/18-remove-file-extensions-from-fil…

…e-names Removed file extensions in middle of file name
Marmzy · Mar 20, 2023 · 2ea27a7 · 2ea27a7
2 parents abcacaa + c37bade
commit 2ea27a7
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diff --git a/src/ROSE_bamToGFF.py b/src/ROSE_bamToGFF.py
@@ -189,7 +189,7 @@ def main() -> None:
     #Outputting per-bin read density
     for newGFF, (bam, gff) in zip(results, product(bam_files, [args.input, args.original])):
         out_df = pd.DataFrame(newGFF, columns=["GENE_ID", "locusLine"] + [f"bin_{n}_{str(Path(bam).name)}" for n in range(1, int(args.matrix)+1)])
-        out_name = check_path(Path(Path(gff).parents[1], "mappedGFF", f"{Path(gff).stem}_{Path(bam).name}_mapped.txt"))
+        out_name = check_path(Path(Path(gff).parents[1], "mappedGFF", f"{Path(gff).stem}_{Path(bam).stem}_mapped.txt"))
         out_df.to_csv(out_name, sep="\t", index=False)
 
 

diff --git a/src/ROSE_mapCollection.py b/src/ROSE_mapCollection.py
@@ -85,7 +85,7 @@ def mapCollection() -> None:
         mappedLoci = []
 
         #Open mapped stitched enhancer loci file as a dataframe
-        mappedGFF = check_file(Path(args.dir, f"{Path(args.stitch).stem}_{Path(bam).name}_mapped.txt"))
+        mappedGFF = check_file(Path(args.dir, f"{Path(args.stitch).stem}_{Path(bam).stem}_mapped.txt"))
         mappedGFF = pd.read_csv(mappedGFF, sep="\t", header=0, comment="#")
 
         #Calculate signal for all stitched enhancer loci