align_draw.pl

#!/usr/bin/perl -w
use strict;
use File::Basename;
use Getopt::Long;

die "Usage:\n	perl $0 -ref <input_reference> -query <input_query> -fig <yes/no> -coverlen 800 -coverrate 6 -outdir ./\n" if @ARGV<2;

my ($refer, $query, $fig, $coverlen, $coverrate, $outdir);
GetOptions(
	"ref:s"=>\$refer,
	"query:s"=>\$query,
	"fig:s"=>\$fig,
	"coverlen:i"=>\$coverlen,
	"coverrate:i"=>\$coverrate,
	"outdir:s"=>\$outdir
);

my $rfname=basename($refer);
my $qfname=basename($query);
#print "$referfilename\n$queryfilename\n";
$fig ||="no";
$coverlen ||=0;
$coverrate ||=0;
$outdir ||=".";

`~/Software/mummer-4.0.0rc1/nucmer -p $outdir/$rfname\_vs_$qfname $refer $query 1>$outdir/$rfname\_vs_$qfname\_mummer.log 2>$outdir/$rfname\_vs_$qfname\_mummer.err`;
`~/Software/mummer-4.0.0rc1/show-coords -rcl $outdir/$rfname\_vs_$qfname.delta > $outdir/$rfname\_vs_$qfname.coords`;
`less $outdir/$rfname\_vs_$qfname.coords |grep "|" |grep "% IDY" -v |awk '\$8>=$coverlen && \$16>=$coverrate' > $outdir/$rfname\_vs_$qfname.coords.cp`;

unless(-z "$outdir/$rfname\_vs_$qfname.coords.cp"){
`perl /home/xzhong/working_data_01/common_bin/fishInWinter.pl -bc 19 -fc 19 $outdir/$rfname\_vs_$qfname.coords.cp $outdir/$rfname\_vs_$qfname.coords > $outdir/$rfname\_vs_$qfname.coords.cp.all.list`;
`less $outdir/$rfname\_vs_$qfname.coords.cp.all.list |awk '{print \$18"\t"\$1"\t"\$2"\t"\$19"\t"\$4"\t"\$5"\t"\$12"\t"\$13}'|sed 's/|/_/g' > $outdir/$rfname\_vs_$qfname.coords.cp.all.list2`;

if ($fig eq "yes"){
my %chash;
open IN, "$outdir/$rfname\_vs_$qfname.coords.cp.all.list2" || die "$!\n";
while(<IN>){
	chomp;
	my @info=split;
	#print "$info[0]\t$info[3]\t$info[6]\t$info[7]\n";
	if (! exists $chash{$info[3]}){
		#print "perl /home/xzhong/common_bin/Draw_scripts/scaffold_pair_svg.pl $outdir/$rfname\_vs_$qfname.coords.list $outdir/$rfname\_vs_$info[3].svg --chr_1 \"$info[0]\" --chr_2 \"$info[3]\" --start_1 1 --end_1 $info[6] --start_2 1 --end_2 $info[7]\n";
		`perl /home/xzhong/common_bin/Draw_scripts/scaffold_pair_svg.pl $outdir/$rfname\_vs_$qfname.coords.cp.all.list2 $outdir/$rfname\_vs_$info[3].svg --chr_1 "$info[0]" --chr_2 "$info[3]" --start_1 1 --end_1 $info[6] --start_2 1 --end_2 $info[7]`;
		$chash{$info[3]}++;
	}		
}
close IN;
}
}