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|
#!/usr/bin/env perl
use strict;
use warnings;
use lib ("/usr/lib/trinityrnaseq/PerlLib");
use DelimParser;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
###############################################################################
#
# Required:
#
# --left <string> left.fq.stats
# --right <string> right.fq.stats
#
# Optional
#
# --sorted flag indicating that entries are lexically sorted
# (this can account for differences in representation by
# reads in either file)
# Unpaired entries are ignored.
#
################################################################################
__EOUSAGE__
;
my $left_stats_file;
my $right_stats_file;
my $sorted_flag = 0;
&GetOptions( 'left=s' => \$left_stats_file,
'right=s' => \$right_stats_file,
'sorted' => \$sorted_flag,
);
unless ($left_stats_file && $right_stats_file) {
die $usage;
}
main: {
my ($left_fh, $right_fh);
print STDERR "-opening $left_stats_file\n";
if ($left_stats_file =~ /\.gz$/) {
open ($left_fh, "gunzip -c $left_stats_file | ") or die $!;
} elsif ($left_stats_file =~ /\.xz$/) {
open(${left_fh}, "xz -cd ${left_stats_file} | ") or die $!;
}
else {
open ($left_fh, $left_stats_file) or die $!;
}
print STDERR "-opening $right_stats_file\n";
if ($right_stats_file =~ /\.gz$/) {
open ($right_fh, "gunzip -c $right_stats_file | ") or die $!;
} elsif ($right_stats_file =~ /\.xz$/) {
open (${right_fh}, "xz -dc ${right_stats_file} | ") or die $!;
}
else {
open ($right_fh, $right_stats_file) or die $!;
}
print STDERR "-done opening files.\n";
my $left_delim_parser = new DelimParser::Reader($left_fh, "\t");
my $right_delim_parser = new DelimParser::Reader($right_fh, "\t");
# print header:
print join("\t", "acc",
"left_acc", "left_median_cov", "left_mean_cov", "left_stdev",
"right_acc", "right_median_cov", "right_mean_cov", "right_stdev",
"median_cov", "mean_cov", "stdev"
) . "\n";
my $left_row = $left_delim_parser->get_row();
my $right_row = $right_delim_parser->get_row();
while (1) {
if ( (! $left_row) || (! $right_row)) {
last;
}
my $left_acc = $left_row->{acc};
my $left_median = $left_row->{median_cov};
my $left_mean = $left_row->{mean_cov};
my $left_stdev = $left_row->{stdev};
my $right_acc = $right_row->{acc};
my $right_median = $right_row->{median_cov};
my $right_mean = $right_row->{mean_cov};
my $right_stdev = $right_row->{stdev};
my $core_acc = $left_acc;
if ($left_acc =~ /^(\S+)\/\d$/) {
$core_acc = $1;
}
my $right_core = $right_acc;
if ($right_acc =~ /^(\S+)\/\d$/) {
$right_core = $1;
}
unless ($right_core eq $core_acc) {
if ($sorted_flag) {
if ($left_acc lt $right_acc) {
$left_row = $left_delim_parser->get_row(); # advance left
}
else {
# advance right
$right_row = $right_delim_parser->get_row();
}
next;
}
else {
die "Error, core accs are not equivalent: [$core_acc] vs. [$right_core] reads, and --sorted flag wasn't used here.";
}
}
print join("\t", $core_acc,
$left_acc, $left_median, $left_mean, $left_stdev,
$right_acc, $right_median, $right_mean, $right_stdev,
sprintf("%.1f", ($left_median + $right_median)/2),
sprintf("%.1f", ($left_mean + $right_mean)/2),
sprintf("%.1f", ($left_stdev + $right_stdev)/2)
) . "\n";
## advance next entries.
$left_row = $left_delim_parser->get_row();
$right_row = $right_delim_parser->get_row();
}
exit(0);
}
|
