gs_raw_replace.pl

#!/usr/bin/env perl
# Ahthor: Zhao
# Date: 2012-05-04
# Purpose: 将gs导出文件的raw数据替换为另一个atv里面的raw数据
# Note: all_raw.txt 为原始数值对照的文件，导出时只选raw data，注释什么不要，
# 可以加快计算

use warnings;
use Data::Table;
use 5.010;
use Smart::Comments;
use Statistics::Basic qw/average/;
use threads;
use Thread::Semaphore;
$cpus      = 10;
$semaphore = new Thread::Semaphore($cpus);

$all_file = 'all_raw.txt';
$name_file = 'name.txt';
@files = glob 'mRNA/*.txt lncRNA/*.txt';

say 'Replace raw data in:';
say join("\n",@files);
say "using coresponding data in $all_file";

$all_tbl = fromTSV($all_file);
$name_tbl = fromTSV($name_file);
$is_group = $name_tbl->nofCol == 2 ? 0 : 1;
foreach $file (@files) {
$semaphore->down();
$thread = async {
  $tbl = fromTSV($file);
  @header = $tbl->header;
  $row_num = $tbl->nofRow - 1;
  foreach $r ( 0 .. $row_num ) {
    $match = $all_tbl->match_pattern('$_->[0] eq "'.$tbl->elm($r,$header[0]).'"');
    unless ( $match->nofRow == 1 ) {
      say "row number not correct for ",$tbl->elm($r,$header[0]);
    }
    %raw_val = ();
    foreach $i ( 0 .. $name_tbl->nofRow - 1 ) {
      if ($file =~ /sample/) {
        if ($is_group == 1) {
          $colID = join('','[',$name_tbl->elm($i,'Sample'),', ',$name_tbl->elm($i,'Group'),'](raw)');
        }
        else{
          $colID = join('','[',$name_tbl->elm($i,'Sample'),'](raw)');
        }
        next if ( $tbl->colIndex($colID) == -1 );

        $colID_all = join('',$name_tbl->elm($i,'Samples'),'(raw)');
        $raw_val = $match->elm(0,$colID_all);
        $tbl->setElm($r,$colID,$raw_val);
      }
      elsif ($file =~ /group/) {
        $gn = $name_tbl->elm($i,'Group');
        $colID = join('','[',$gn,'](raw)');
        next if ( $tbl->colIndex($colID) == -1 );

        $colID_all = join('',$name_tbl->elm($i,'Samples'),'(raw)');
        push(@{$raw_val{$gn}}, $match->elm(0,$colID_all));
      }
      else {
        die 'OMG!';
      }
    }
    foreach $gn ( keys %raw_val ) {
      $colID = join('','[',$gn,'](raw)');
      $tbl->setElm($r,$colID,average($raw_val{$gn}) * 1);
    }
    if ( $r % 500 == 0 ) {
      &bar($r,$row_num);
      say $file;
    }
  }
  outputTSV($tbl,$file.'.mo');
  $file =~ s/\(/\\(/g;
  $file =~ s/\)/\\)/g;
  `grep \\# $file > $file.com`;
  `cat $file.mo >> $file.com`;
  `rm -f $file.mo`;
  say "$file done";
  $semaphore->up();
};
$thread->detach();
}

&waitquit;

sub waitquit {
    my $num = 0;
    while ( $num < $cpus ) {
        $semaphore->down();
        $num++;
    }
    $semaphore->up($cpus);
}

sub fromTSV{
  my $file = $_[0] || die "File not declared!";
  my %fileGuessOS = ( 0 => "UNIX", 1 => "DOS", 2 => "MAC" );
  print "read $file in ",$fileGuessOS{Data::Table::fromFileGuessOS($file)}," format.\n";
  return Data::Table::fromTSV($file,1,undef,
      {OS=>Data::Table::fromFileGuessOS($file),
      skip_pattern=>'^\s*#'});
}

sub outputTSV{
  my ($table,$file,$header) = @_;
  print "outputTSV() parameter ERROR!" unless defined $table;
  $header = defined $header ? $header : 1;
  if( defined $file ){
    $table->tsv($header, {OS=>0, file=>$file});
  }else{
    print $table->tsv($header, {OS=>0, file=>undef});
  }
  return $table->tsv($header, {OS=>0, file=>undef});
}

sub bar {
  local $| = 1;
  my $i = $_[0] || return 0;
  my $n = $_[1] || return 0;
  print "\r["
    . ( "#" x int( ( $i / $n ) * 50 ) )
    . ( " " x ( 50 - int( ( $i / $n ) * 50 ) ) ) . "]";
  printf( "%2.1f%%", $i / $n * 100 );
  local $| = 0;
}