split the abacas joined chromosomes

[yzzhang]

Hi, All. I just tried to align my contigs to a genome which has 9 chromosomes using ABACAS. I followed the PAGIT toolkit published on nature protocol, but after I joined the chromosomes together as required by abacas, I could not split the files, the script in the PAGIT "split2multifasta.pl did not work. Does some one have suggestions? Thank you.
yun

[seb567]

Originally Posted by yzzhang

Hi, All. I just tried to align my contigs to a genome which has 9 chromosomes using ABACAS. I followed the PAGIT toolkit published on nature protocol, but after I joined the chromosomes together as required by abacas, I could not split the files, the script in the PAGIT "split2multifasta.pl did not work. Does some one have suggestions? Thank you.
yun

Can you provide details about the statement "PAGIT split2multifasta.pl did not work" ?

[yzzhang]

I looked through the split2multifasta.pl script, there were only few lines like that
use strict;


if (scalar(@ARGV)<5) {
die "usage: <Reference File> <ordered ABACAS query file> <resultName> <crunchfile> <Tag>\n\nThis script will split the query file accordinly to the reference, assuming the reference got processed with joinMultifasta.pl.\n";
}

my $spacer;
my $splitinfo = shift;
my $queryFile = shift;
my $crunchFile = shift;
my $resultName = shift;

print "Sorry, this script has not yet be included properly to the PAGIT distribution.\n";
.I email the author, and he kindly sent me the script and now I can use this pipeline now.

[flipwell]

Has anyone had any trouble running this script? When I try to run it nothing happens. I don't get any errors it just seems to sit there and produce nothing. Does it take a long time to run?

Thanks