Add --chrprefix

tanghaibao · Aug 9, 2024 · 3689e1c · 3689e1c
1 parent afb7b2d
commit 3689e1c
Showing 1 changed file with 4 additions and 0 deletions.
diff --git a/jcvi/formats/bed.py b/jcvi/formats/bed.py
@@ -593,6 +593,7 @@ def format(args):
     Re-format BED file, e.g. switch sequence ids.
     """
     p = OptionParser(format.__doc__)
+    p.add_argument("--chrprefix", help="Add prefix to seqid")
     p.add_argument("--prefix", help="Add prefix to name column (4th)")
     p.add_argument("--switch", help="Switch seqids based on two-column file")
     p.set_outfile()
@@ -604,11 +605,14 @@ def format(args):
     (bedfile,) = args
     switch = DictFile(opts.switch, delimiter="\t") if opts.switch else None
     prefix = opts.prefix
+    chrprefix = opts.chrprefix
     bed = Bed(bedfile)
     with must_open(opts.outfile, "w") as fw:
         for b in bed:
             if prefix:
                 b.accn = prefix + b.accn
+            if chrprefix:
+                b.seqid = chrprefix + b.seqid
             if switch and b.seqid in switch:
                 b.seqid = switch[b.seqid]
             print(b, file=fw)