cli.gc: bugfix

golobor · golobor · commit 0eed1ad87570 · 2021-01-27T17:20:41.000+01:00
diff --git a/cooltools/cli/genome.py b/cooltools/cli/genome.py
@@ -72,7 +72,7 @@ def gc(bins_path, fasta_path, mapped_only):
             "Some chromosomes mentioned in {}"
             " are not found in {}".format(bins_path, fasta_path)
         )
-    bins["GC"] = bioframe.tools.frac_gc(bins, fasta_records, mapped_only)
+    bins["GC"] = bioframe.genomeops.frac_gc(bins, fasta_records, mapped_only, return_input=False)
     print(bins.to_csv(sep="\t", index=False))
 
 

Original file line number	Diff line number	Diff line change
`@@ -72,7 +72,7 @@ def gc(bins_path, fasta_path, mapped_only):`
`72`	`72`	`"Some chromosomes mentioned in {}"`
`73`	`73`	`" are not found in {}".format(bins_path, fasta_path)`
`74`	`74`	`)`
`75`		`- bins["GC"] = bioframe.tools.frac_gc(bins, fasta_records, mapped_only)`
	`75`	`+ bins["GC"] = bioframe.genomeops.frac_gc(bins, fasta_records, mapped_only, return_input=False)`
`76`	`76`	`print(bins.to_csv(sep="\t", index=False))`
`77`	`77`
`78`	`78`