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Commit 4486f9b2 authored by tjc's avatar tjc
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tweak to run emma

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@2123 ee4ac58c-ac51-4696-9907-e4b3aa274f04
parent 8843b73d
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......@@ -2,6 +2,9 @@
# This script needs one argument - a file of file names.
PATH=/nfs/disk100/pubseq/emboss/bin/:$PATH
export PATH
PERL_PROG='
use strict;
......@@ -20,9 +23,12 @@ if (-e $file)
my $msf_file = "$file.fasta_msf";
my $seqnum = 1;
printf "$msf_file\n";
open(LIST_FILE,$file);
while(my $line = <LIST_FILE>)
{
printf "$line\n";
chomp($line);
#
......@@ -46,6 +52,10 @@ if (-e $file)
close EMBOSS;
system "jalview", "$msf_file";
}
else
{
die "$file does not exist";
}
'
PERL_PROG_FASTA='
......@@ -220,12 +230,14 @@ while (defined ($file = <>)) {
}
}'
if [ $# != 1 ]
then
perl -w -e "$PERL_PROG" "$@"
else
perl -w -e "$PERL_PROG_FASTA" "$@"
fi
#if [ $# != 1 ]
#then
# perl -w -e "$PERL_PROG" "$@"
#else
# perl -w -e "$PERL_PROG_FASTA" "$@"
#fi
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