Force unix-style line endings on tsv outputs

open2c · Feb 1, 2024 · 1c13d84 · 1c13d84
1 parent 4bcdb07
commit 1c13d84
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Showing 3 changed files with 16 additions and 5 deletions.
diff --git a/src/cooler/cli/digest.py b/src/cooler/cli/digest.py
@@ -71,6 +71,8 @@ def digest(chromsizes, fasta, enzyme, out, header, rel_ids):
         f = open(out, "w")
 
     if header:
-        frags[0:0].to_csv(f, sep="\t", index=False, header=True)
-    frags.to_csv(f, sep="\t", index=False, header=False)
+        frags[0:0].to_csv(
+            f, sep="\t", line_terminator='\n', index=False, header=True
+        )
+    frags.to_csv(f, sep="\t", line_terminator='\n', index=False, header=False)
     f.flush()
diff --git a/src/cooler/cli/dump.py b/src/cooler/cli/dump.py
@@ -280,13 +280,20 @@ def dump(
         if is_first_chunk:
             if header:
                 chunk[0:0].to_csv(
-                    f, sep="\t", index=False, header=True, float_format=float_format
+                    f,
+                    sep="\t",
+                    line_terminator='\n',
+                    index=False,
+                    header=True,
+                    float_format=float_format,
+                    na_rep=na_rep,
                 )
             is_first_chunk = False
 
         chunk.to_csv(
             f,
             sep="\t",
+            line_terminator='\n',
             index=False,
             header=False,
             float_format=float_format,

diff --git a/src/cooler/cli/makebins.py b/src/cooler/cli/makebins.py
@@ -54,6 +54,8 @@ def makebins(chromsizes, binsize, out, header, rel_ids):
         f = open(out, "w")
 
     if header:
-        bins[0:0].to_csv(f, sep="\t", index=False, header=True)
-    bins.to_csv(f, sep="\t", index=False, header=False)
+        bins[0:0].to_csv(
+            f, sep="\t", line_terminator='\n', index=False, header=True
+        )
+    bins.to_csv(f, sep="\t", line_terminator='\n', index=False, header=False)
     f.flush()