30d1e434dcd5b313f393eac770c8da2d4323d54f
angie
  Fri Oct 13 11:45:13 2023 -0700
Adding download & usher tree build scripts for several non-SARS-CoV-2 viruses.
mpxv has been going for over a year, rsv & dengue for some months now.  fluA is an incomplete work in progress,
complicated by having 8 segments, greater distances, and different subtyping schemes for different segments and even for different types within the segments.

diff --git src/hg/utils/otto/fluA/splitGbff.pl src/hg/utils/otto/fluA/splitGbff.pl
new file mode 100755
index 0000000..10452e0
--- /dev/null
+++ src/hg/utils/otto/fluA/splitGbff.pl
@@ -0,0 +1,22 @@
+#!/usr/bin/env perl
+
+# Read a series of GenBank flat file LOCUS records and write each one to a file.
+
+use warnings;
+use strict;
+
+my $outF;
+
+while (<>) {
+  if (/^LOCUS\s+(\w+)/) {
+    my $acc = $1;
+    close $outF if ($outF);
+    open($outF, ">$acc.gbff") || die;
+    print $outF $_;
+  } elsif ($outF) {
+    print $outF $_;
+  } else {
+    die "Expected input to begin with a LOCUS line but got this:\n$_";
+  }
+}
+close $outF if ($outF);