From fea3d79a60d37b7feb9b491f14412ea8e71b89b5 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 22 Jun 2004 10:10:39 +0000
Subject: [PATCH] correct data dir
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@1675 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
etc/run_jalview | 16 +++++++++++++++-
1 file changed, 15 insertions(+), 1 deletion(-)
diff --git a/etc/run_jalview b/etc/run_jalview
index dd8e78383..673cf26ef 100755
--- a/etc/run_jalview
+++ b/etc/run_jalview
@@ -71,10 +71,24 @@ sub process_fasta
die "cannot understand $fasta_results_file\n";
}
+
if (! -e $sequence_file) {
- die "cannot find $sequence_file\n";
+ if ($feature_file =~ /(.*)(\/jalview\/)(.+)$/)
+ {
+ $sequence_file = "$1/$sequence_file";
+ if (! -e $fasta_results_file &&
+ ! -e "$fasta_results_file.gz")
+ {
+ $fasta_results_file = "$1/$fasta_results_file";
+ }
+ }
+ if (! -e $sequence_file)
+ {
+ die "cannot find $sequence_file\n";
+ }
}
+
my $fasta_seq_for_alignment = "";
open SEQ_FILE, $sequence_file or die "cannot open $sequence_file: $!\n";
--
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