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Revision 1.1 - (download) (as text) (annotate)
Wed Jun 18 15:49:33 2008 UTC (11 years, 4 months ago) by arodri7
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, myrast_rel40, mgrast_dev_05262011, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, mgrast_version_3_2, mgrast_dev_12152011, mgrast_dev_06072011, rast_rel_2008_09_30, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2014_0729, mgrast_dev_02212011, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, rast_rel_2009_02_05, rast_rel_2011_0119, mgrast_rel_2008_0625, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_1, mgrast_dev_03312011, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, rast_rel_2008_10_09, mgrast_dev_04012011, rast_release_2008_09_29, mgrast_rel_2008_0806, mgrast_rel_2008_0923, mgrast_rel_2008_0919, rast_rel_2009_07_09, rast_rel_2010_0827, mgrast_rel_2008_1110, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, mgrast_rel_2008_0917, rast_rel_2008_10_29, mgrast_dev_04052011, mgrast_dev_02222011, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
update changes

use strict;

use FIG;
my $fig = new FIG;
use FigFam;
my $procs = 11;

my $usage = "usage: connect_pdb_to_FIGfams FigfamsData OutDir pdb_file";

my($ff_data,$outD,$pdbaa);
(
 ($ff_data  = shift @ARGV) &&
 ($outD     = shift @ARGV) &&
 ($pdbaa    = shift @ARGV)
)
    || die $usage;

&FIG::verify_dir($outD);
open(PDB,"<$pdbaa") || die "where is pdbaa?";

my @procs = &start_procs("connect_PDB_to_FIGfams_worker $ff_data $outD",$procs);

my $nextP = 0;
$/ = "\n>";
while (defined(my $x = <PDB>))
{
    if ($x =~ /^>?(\S+)[^\n]*\n(.*?)>/s)
    {
	my $id = $1;
	my $seq = $2;
	$seq =~ s/\s//g;
	my $n = ($seq =~ tr/acdefghiklmnpqrstvwyACDEFGHIKLMNPQRSTVWY//);
	if ($n > 20)
	{
	    my $fh = $procs[$nextP];
	    print $fh "$id\t$seq\n";
	    $nextP = ($nextP == $#procs) ? 0 : $nextP+1;
	}
    }
}
$/ = "\n";

&close_procs(\@procs);
print STDERR "closed processes\n";

my @out;
for (my $i=1; ($i <= $procs); $i++)
{
    open(TMP,"<$outD/$i") || die "could not open $outD/$i";
    while (defined($_ = <TMP>))
    {
	chop;
	push(@out,[split(/\t/,$_)]);
    }
    close(TMP);
}

my @sorted = sort { ($a->[0] cmp $b->[0]) or ($b->[12] <=> $a->[12]) } @out;
foreach $_ (@sorted)
{
    print join("\t",@$_),"\n";
}

sub start_procs {
    my($cmd,$procsN) = @_;

    my @procs = ();
    open(F1,"| $cmd 1") || die 1;
    my $ofh = select F1; $| = 1; select $ofh;
    push(@procs,\*F1);
    print STDERR "starting process 1\n";

    $procsN--; if ($procsN == 0) { return @procs }
    open(F2,"| $cmd 2") || die 2;
    my $ofh = select F2; $| = 1; select $ofh;
    push(@procs,\*F2);
    print STDERR "starting process 2\n";

    $procsN--; if ($procsN == 0) { return @procs }
    open(F3,"| $cmd 3") || die 3;
    my $ofh = select F3; $| = 1; select $ofh;
    push(@procs,\*F3);
    print STDERR "starting process 3\n";

    $procsN--; if ($procsN == 0) { return @procs }
    open(F4,"| $cmd 4") || die 4;
    my $ofh = select F4; $| = 1; select $ofh;
    push(@procs,\*F4);
    print STDERR "starting process 4\n";

    $procsN--; if ($procsN == 0) { return @procs }
    open(F5,"| $cmd 5") || die 5;
    my $ofh = select F5; $| = 1; select $ofh;
    push(@procs,\*F5);
    print STDERR "starting process 5\n";

    $procsN--; if ($procsN == 0) { return @procs }
    open(F6,"| $cmd 6") || die 6;
    my $ofh = select F6; $| = 1; select $ofh;
    push(@procs,\*F6);
    print STDERR "starting process 6\n";

    $procsN--; if ($procsN == 0) { return @procs }
    open(F7,"| $cmd 7") || die 7;
    my $ofh = select F7; $| = 1; select $ofh;
    push(@procs,\*F7);
    print STDERR "starting process 7\n";

    $procsN--; if ($procsN == 0) { return @procs }
    open(F8,"| $cmd 8") || die 8;
    my $ofh = select F8; $| = 1; select $ofh;
    push(@procs,\*F8);
    print STDERR "starting process 8\n";

    $procsN--; if ($procsN == 0) { return @procs }
    open(F9,"| $cmd 9") || die 9;
    my $ofh = select F9; $| = 1; select $ofh;
    push(@procs,\*F9);
    print STDERR "starting process 9\n";

    $procsN--; if ($procsN == 0) { return @procs }
    open(F10,"| $cmd 10") || die 10;
    my $ofh = select F10; $| = 1; select $ofh;
    push(@procs,\*F10);
    print STDERR "starting process 10\n";

    $procsN--; if ($procsN == 0) { return @procs }
    open(F11,"| $cmd 11") || die 11;
    my $ofh = select F11; $| = 1; select $ofh;
    push(@procs,\*F11);
    print STDERR "starting process 11\n";

    $procsN--; if ($procsN == 0) { return @procs }
    open(F12,"| $cmd 12") || die 12;
    my $ofh = select F12; $| = 1; select $ofh;
    push(@procs,\*F12);
    print STDERR "starting process 12\n";

    $procsN--; if ($procsN == 0) { return @procs }
    open(F13,"| $cmd 13") || die 13;
    my $ofh = select F13; $| = 1; select $ofh;
    push(@procs,\*F13);
    print STDERR "starting process 13\n";

    $procsN--; if ($procsN == 0) { return @procs }
    open(F14,"| $cmd 14") || die 14;
    my $ofh = select F14; $| = 1; select $ofh;
    push(@procs,\*F14);
    print STDERR "starting process 14\n";

    return @procs;
}

sub close_procs {
    my($procs) = @_;
    my $proc;

    for (my $i=0; ($i < @$procs); $i++)
    {
	print STDERR "CLOSING ",$i+1,"\n";
	my $fh = $procs->[$i];
	print $fh "x\n";
	close($fh);
	print STDERR "CLOSED ",$i+1,"\n";
    }
}



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