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|
#!/usr/bin/perl
use strict;
use warnings;
use Getopt::Long;
#use Compress::Zlib;
#my $opt_n;
#GetOptions("n" => \$opt_n);
my $opt_prefix=`date +%Y%m%d%H%M%S`;
chomp $opt_prefix;
my $opt_gz;
my $opt_1origin=0;
my $opt_fq=0;
#print $opt_prefix,"\n";
#exit 1;
GetOptions(
"p=s" => \$opt_prefix,
"q" => \$opt_fq,
"1origin"=>\$opt_1origin
);
my $ext="fa";
if($opt_fq){
$ext = "fq";
}
#GetOptions("p=s" => \$opt_prefix, "z" => \$opt_gz);
$opt_gz=0;
if(@ARGV != 2){
printf STDERR ("USAGE: <this> <in.fa> <int (number of partitions)>\n");
printf STDERR ("\t[-p <prefix>: prefix to the outputs. default is yymmddhhmmss]\n");
printf STDERR ("\t[-1origin: for file naming\n");
printf STDERR ("\t[-q : regard input as in fastq]\n");
# printf STDERR ("\t[-z: output gz compressed file instead of uncompressed fasta file]\n");
#printf STDERR ("\t[-n (name: output only names , not sequences)\n");
exit 1;
}
#printf("%s\n", $ARGV[0]);
#printf("%s\n", $ARGV[1]);
#exit 1;
my $in_fa = $ARGV[0];
chomp $in_fa;
#my $IN_FA;
#if($in_fa eq '-'){
# open $IN_FA,"<",STDIN or die "cannot open $in_fa : $!\n";
#}
#else{
open my $IN_FA,"<".$in_fa or die "cannot open $in_fa : $!\n";
#}
my $partitions = $ARGV[1];
if($partitions !~ /^\+?\d+$/){
printf STDERR ("nth must be an integer\n");
exit 1;
}
my @out;
for(my $i=0; $i<$partitions; ++$i){
if($opt_gz){
# $out[$i] = gzopen(sprintf("%s_%04d.fa.gz",$opt_prefix,$i),"wb") or die "cannot open output file:$!\n";
}
else{
if($opt_1origin){
open $out[$i],">",sprintf("%s_%04d.$ext",$opt_prefix,$i+1) or die "cannot open output file:$!\n";
}
else{
open $out[$i],">",sprintf("%s_%04d.$ext",$opt_prefix,$i) or die "cannot open output file:$!\n";
}
}
}
my $counter=-1;
my $name = <$IN_FA>;
while(!eof($IN_FA)){
++$counter;
chomp $name;
my $tmp_name = $name;
my $bases="";
my $opts="";
my $qvs="";
if(!$opt_fq){
while(!eof($IN_FA) && (($name = <$IN_FA>) !~ /^>/)){
chomp $name;#bases
$bases .= $name;
}
}
else{
while(!eof($IN_FA) && (($name = <$IN_FA>) !~ /^\+/)){
chomp $name;#bases
$bases .= $name;
}
chomp $name;
$opts = $name;
while(!eof($IN_FA) && (($name = <$IN_FA>) !~ /^\@/)){
chomp $name;#qvs
$qvs .= $name;
}
if(length($bases) != length($qvs)){
printf STDERR ("|bases| != |qvs|: %d %d\n",length($bases),length($qvs));
exit(1);
}
}
#next if ($counter % $mod != $nth);
my $fh = $out[$counter % $partitions];
if($opt_gz){
# $fh->gzwrite(sprintf("%s\n",$tmp_name));
# $fh->gzwrite(sprintf("%s\n",$bases));
}
else{
printf $fh ("%s\n",$tmp_name);
printf $fh ("%s\n",$bases);
if($opt_fq){
printf $fh ("%s\n",$opts);
printf $fh ("%s\n",$qvs);
}
}
#printf $out[$counter % $partitions] ("%s\n",$tmp_name);
#printf $out[$counter % $partitions] ("%s\n",$bases);
#my $num=70;
#my $loop = length($bases);
#for(my $stt=0; $stt < $loop; $stt += $num){
# printf("%s\n",substr($bases,$stt,$num));
#}
}
close $IN_FA;
for(my $i=0; $i<$partitions; ++$i){
if($opt_gz){
# $out[$i]->gzclose;
}
else{
close $out[$i];
}
}
|
