银河星尘

#!/bin/bash
echo $1
#find $1/*.sp |xargs cat|wc -l|tee $1.wc
find $1/*.sp |xargs cat|awk '{print $6}'|perl -lane 'END { print "$b" } $b+=$_'|tee $1.len

#!/bin/bash
echo $1
find $1/*.soaplst|xargs awk {'print $3'}|xargs cat|awk '{print $6}'|perl -lane 'END { print "$b" } $b+=$_'|tee $1.len

find *.glflst.0|while read a;do b=`echo $a|sed -n 's/^\(.\{1,\}\)\.\w/\1/p'`;echo [$b];./t.pl $a > $b;done

#!/usr/bin/perl -w
use strict;
use warnings;
while (<>) {
        my $line=$_;
        my $name=(split /\//)[-1];
        #print $name;
        $name =~ /GP(\d+)_C.*\.glf/;
        next if $1 >=53;
        #print $1,"\t",$name;
        print $line;
}

awk '{print $1}' ../chr.len \
|while read a;do find ./$a/*.psnp\
|perl -lane '/^(.+?)_(\d+)\.psnp/;$a=$2;$a="00".$a if length($a)==1;$a="0".$a if length($a)==2;$a="z" if length($a)==0;print "$a\t$_"'\
|sort|awk '{print $2}'>>./$a.psnplst;done

find -name *.fq.gz|while read a;do b=`basename $a`;
c=`perl -lae '$_=$ARGV[0];s/\.gz$//;print' $b`;
echo $c;gzip -dc $a > ./0rawfqgz/$c;
done &

awk '$10>100 {print $10}' /ifs1/GAG/watermelon/soapg45/soapg/soap/PE/100214_I646_FC617B1AAXX_L4_WATxozRANDIAAPE_1.fq.soap
 |perl -lane 'if ($_ < 200) {$a=$_-100} else {$a=200-$_} print "$a\t$_"'
 |perl -lane 'BEGIN {my %a} ($x)=split /\t/; ++$a{$x};
  {print "$_\t$a{$_}" for sort {$a <=> $b} keys %a};print "-"x80'

perl -lane '@a=split /\t/;open I,"<soap.lst";@l=<I>;close I;
 @c=grep /$a[1]/,@l;print "[",$a[0],"]\t[",$a[1],"]\n",@c,"\n";
 open O,">>$a[0]/soaps.lst";print O @c;close O;' sample.lst

perl -lane '@a=split /\t/;print $a[0],"\t",$a[1],"\n";
open O,">$a[0]/run${a[0]}.sh";
print O "#\$ -cwd -r y -l vf=500M\n#\$ -o $a[0]/l.log -e $a[0]/l.err\n#\$ -v PERL5LIB,PATH,PYTHONPATH,LD_LIBRARY_PATH\n./soapInDel -s $a[0]/soaps.lst -f /ifs1/GAG/population/project/Watermelon_population/watermelon_v2_888/watermelon.merge.fa -o $a[0]/indel-result.list";
close O' sample.lst

perl -lane '
BEGIN {	my ($last,%c)=($F[0]);}
if ($F[0] eq $last) {
	if (keys %c < 3) {
		(undef,$gi)=split "\\|",$F[1];
		unless ($c{$F[1]}) {
			chomp($a = `./getinfo.sh $gi`) or chomp($a = `./getinfo0.sh $gi`);
			splice @F,2,0,$a;
			print join "\t",@F;
		}
		++$c{$F[1]};
	}
} else {
	$last=$F[0];
	%c=();
	if (keys %c < 3) {
		(undef,$gi)=split "\\|",$F[1];
		chomp($a = `./getinfo.sh $gi`) or chomp($a = `./getinfo0.sh $gi`);
		splice @F,2,0,$a;
		print join "\t",@F;
		++$c{$F[1]};
	}
}
' files/FC61L0PAAXX_L5_TUBhhsRBZDIAAPE_1.blast |les

#!/bin/bash
BLASTDB=/blast/BLASTDB/taxdb:/blast/BLASTDB/asndb /blast/bin/blastdbcmd -db nt -outfmt "%T|%S|%L|%t|%l" -target_only -entry $1

#!/bin/bash
BLASTDB=/blast/BLASTDB/taxdb:/blast/BLASTDB/asndb /blast/bin/blastdbcmd -db nt -outfmt "%T|NA|NA|%t|%l" -target_only -entry $1