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#!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
#######################################################################
#
# Required:
#
# --matrix <string> replicates.TMM_normalized.fpkm.matrix
#
# --samples_file <string> description of sample-to-replicate mapping (tab-delimited)
#
# ex.
# condA repA1
# condA repA2
# condB repB1
# condB repB2
#
#
# Optional:
#
# --avg_log_val yield exp(avg(log(replicates))) instead of default: avg(replicates)
#
#
#######################################################################
__EOUSAGE__
;
my $matrix_file;
my $use_avg_log_val = 0;
my $samples_file;
my $help_flag;
my $test_flag = 0;
&GetOptions("matrix=s" => \$matrix_file,
"samples_file=s" => \$samples_file,
"avg_log_val" => \$use_avg_log_val,
"help|h" => \$help_flag,
"test|T" => \$test_flag,
);
if ($help_flag) {
die $usage;
}
unless (($matrix_file && $samples_file) || $test_flag) {
die $usage;
}
main: {
if ($test_flag) {
$matrix_file = "test.matrix";
$samples_file = "test.samples";
&write_test_data($matrix_file, $samples_file);
}
my $out_prefix = "$matrix_file.avg_reps";
if ($use_avg_log_val) {
$out_prefix .= ".byLog";
}
my $out_matrix = $out_prefix . ".matrix";
my $out_rscript = $out_prefix . ".Rscript";
open (my $ofh, ">$out_rscript") or die "Error, cannot write to $out_rscript";
print $ofh <<__EORSCRIPT__;
samples = read.table("$samples_file", header=F, check.names=F)
sample_types = as.vector(unique(samples[,1]))
nsamples = length(sample_types)
data = read.table("$matrix_file", header=T, row.names=1, com='', nrows=10000, check.names=F)
classes = sapply(data,class)
data = read.table("$matrix_file", header=T, row.names=1, com='', colClasses=classes, check.names=F)
data = as.matrix(data)
sample_factoring = rep(NA, ncol(data))
sample_expr_matrix = matrix(ncol=nsamples, nrow=nrow(data))
colnames(sample_expr_matrix) = sample_types
rownames(sample_expr_matrix) = rownames(data)
for (i in 1:nsamples) {
sample_type = sample_types[i]
rep_indices = samples[,1] \%in% sample_type
#print(paste("rep_indices:", rep_indices))
rep_names = as.vector(samples[rep_indices,2])
cat("sample_type: ", sample_type, "\n")
cat("rep_names: ", rep_names, "\n")
col_indices = colnames(data) \%in% rep_names
#print(col_indices);
if (sum(col_indices) == 0) {
stop(cat("Error, no columns found matching sample type:", sample_type, "with replicate names:", rep_names))
}
if (sum(col_indices) != length(rep_names)) {
found_colnames = colnames(data)[col_indices]
missing = rep_names[ ! rep_names \%in% found_colnames]
cat ("Error, not all replicates accounted for. Found only", sum(col_indices), "columns but have", length(rep_names), "replicates:", rep_names, "for sample:", sample_type, "missing:", missing)
stop()
}
sample_factoring[col_indices] = sample_type
avg_vals = NULL
if ($use_avg_log_val) {
avg_vals = apply(data[,col_indices, drop=F], 1, function(x) exp((mean(log(x+1)))) -1)
} else {
avg_vals = apply(data[,col_indices, drop=F], 1, mean)
}
sample_expr_matrix[,i] = sprintf("%.3f", avg_vals)
}
write.table(sample_expr_matrix, "$out_matrix", quote=F, sep="\t")
__EORSCRIPT__
;
my $cmd = "R --no-save --no-restore --no-site-file --no-init-file -q < $out_rscript";
my $ret = system($cmd);
if ($ret) {
die "Error, cmd: $cmd died with ret $ret";
}
print "\n\nDone. See output: $out_matrix\n\n";
exit(0);
}
####
sub write_test_data {
my ($test_matrix_file, $test_samples_file) = @_;
open (my $ofh, ">$test_matrix_file") or die $!;
print $ofh
"S1 S2 S3 S4 S5 C1 C2 C3 C4 C5
1 456 726 380 554 184 9 7 3 9 7
2 34 49 43 35 30 18 15 11 23 7
3 22 17 35 17 18 45 127 73 78 93
4 11 6 11 4 7 52 57 44 27 19
5 18 19 12 25 17 193 130 69 137 164
6 41 71 38 59 36 37 45 24 41 16
7 2 11 17 12 10 152 230 137 185 154
8 6 20 26 25 22 2 4 0 1 2
9 12 28 11 13 16 4 15 6 12 12
10 34 31 13 30 25 8 3 10 12 16
";
close $ofh;
open ($ofh, ">$test_samples_file") or die $!;
print $ofh
"S S1
S S2
S S3
S S4
S S5
C C1
C C2
C C3
C C4
C C5
";
return;
}
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