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#!/usr/bin/perl
#############################################################################
#
# makeidx.pl
#
# format genomic sequence or protein sequence database
# to be used by spaln
#
#
# Osamu Gotoh, ph.D. (-2001)
# Saitama Cancer Center Research Institute
# 818 Komuro, Ina-machi, Saitama 362-0806, Japan
#
# Osamu Gotoh, Ph.D. (2001-)
# National Institute of Advanced Industrial Science and Technology
# Computational Biology Research Center (CBRC)
# 2-41-6 Aomi, Koutou-ku, Tokyo 135-0064, Japan
#
# Osamu Gotoh, Ph.D. (2003-2012)
# Department of Intelligence Science and Technology
# Graduate School of Informatics, Kyoto University
# Yoshida Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
#
# Copyright(c) Osamu Gotoh <<o.gotoh@aist.go.jp>>
#
#___________________________________________________________________________
#
# Usage: makeidx.pl [-ianp] [-s src_dir] [-d dest_dir] [-g] fasta_file[.gz]
# -i: Make index
# -a: Make block info of aa sequences
# -n: Make block info of genomic sequence for DNA queries
# -p: Make block info of genomic sequence for aa queries
#
# Examples:
#
# % makeidx.pl -inp -g dictdisc_g.gf.gz
# % makeidx.pl -ia dictdisc.faa.gz
#
###############################################################################
use strict;
use FindBin;
my $scriptpath = $FindBin::Bin;
my ($obj, $gz, $opt, $compress) = ('i');
my $makefile = "./Makefile";
my $src_dir = "./";
sub usage {
print "Usage: makeidx.pl [-ianp] [-s src_dir] [-d seqdb/] [-g] fasta_file[.gz]\n";
exit(1);
}
while ($_ = $ARGV[0], /^-/) {
shift;
if (/^-h/) {&usage;}
elsif (/^-s(\S+)/) {$src_dir = $1;} # define src_dir
elsif (/^-s/) {$src_dir = shift;}
elsif (/^-g/) {$opt .= '-g '; $compress = 1;}
elsif (/^(-y\S+)/ || /^(-X\S+)/ || /^(-R\S*)/ || /^(-D\S*)/)
{$opt .= "$1 ";}
elsif (/^-(\w+)/) {$obj .= lc($1);} # [a|n|p|np]
}
my $fsrc = shift;
unless (-s $fsrc) {
$src_dir .= '/' if (substr($src_dir, -1, 1) ne '/');
$fsrc = "$src_dir$fsrc";
exit(1) unless (-s $fsrc);
}
my $sl = rindex($fsrc, '/');
my $fa = substr($fsrc, $sl + 1);
#### examine free disk space
open(DF, "df |") or die "Can't run df !\n";
while (<DF>) {
chomp;
my @a = split;
my $mp = pop(@a);
next if ($mp ne "/data");
my $pc = pop(@a);
chop($pc);
die "$mp about to be full !\n" if ($pc >= 99);
}
close(DF);
#### start of main ####
print STDERR "$fa $obj\n";
my $fnm = $fa;
my @ind = ('i', 'a', 'n', 'p');
my @ext = ('idx', 'bka', 'bkn', 'bkp');
my $dot = rindex($fa, '.');
&usage unless ($dot > 0);
my $src_ext = substr($fa, $dot + 1);
my $fnm = substr($fa, 0, $dot);
if (($gz = $src_ext eq "gz")) {
$dot = rindex($fnm, '.');
&usage unless ($dot > 0);
$src_ext = substr($fnm, $dot + 1);
}
my $bdy = substr($fnm, 0, $dot);
my @exp = ();
for (my $i = 0; $i < @ind; ++$i) {
next if (index($obj, $ind[$i]) < 0);
my $ffn = $bdy . '.' . $ext[$i];
if ($i == 0) {
my $odr = $bdy . '.odr';
unlink($odr) if (-e $odr && -M $odr > -M $fsrc);
}
if (-s $ffn) {
if (-M $ffn > -M $fsrc) {
unlink($ffn);
++$exp[$i];
}
} else {
$ffn .= '.gz';
if (-s $ffn) {
if (-M $ffn > -M $fsrc) {
unlink($ffn);
++$exp[$i];
}
} else {
++$exp[$i];
}
}
}
exit(0) unless (@exp);
for (my $i = 0; $i < @ind; ++$i) {
next unless ($exp[$i]);
if ($i == 0) {&makeidx($fa);}
else {
my $ffn = $bdy . '.' . $ext[$i];
&makeblk($fa, $ffn);
}
}
#### end of main ####
sub makeidx {
my $fa = shift;
my $cmd = "makdbs -K";
$cmd .= ($src_ext eq 'fa' || $src_ext eq 'faa')? 'A': 'D';
$cmd .= ' -g' if ($compress);
$cmd .= " $fa";
system($cmd);
}
sub makeblk {
my ($fa, $blk) = @_;
my $cmd = "$scriptpath/makblk.pl -W$blk $opt $fa";
print STDERR "$cmd\n";
system($cmd);
}
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