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|
#!/usr/bin/env perl
use strict;
use warnings;
use lib ("/usr/lib/trinityrnaseq/PerlLib");
use SAM_reader;
use SAM_entry;
my $usage = "\n\n\tusage: $0 transcript_aligned.bam top_percent=10\n\n";
my $bam_file = $ARGV[0] or die $usage;
my $top_percent = $ARGV[1] || 10;
main: {
my %transcript_to_orients;
my $sam_reader = new SAM_reader($bam_file);
print STDERR "-parsing file: $bam_file\n";
while (my $sam_entry = $sam_reader->get_next()) {
if ($sam_entry->is_proper_pair() && $sam_entry->is_first_in_pair()) {
my $orient = $sam_entry->get_query_strand();
my $trans_name = $sam_entry->get_scaffold_name();
#print STDERR "$trans_name\t$orient\n";
$transcript_to_orients{$trans_name}->{$orient}++;
}
}
print STDERR "-done parsing file, examining orientations of reads.\n";
## sum them up.
my @transcripts = keys %transcript_to_orients;
foreach my $transcript (@transcripts) {
my $orient_plus = $transcript_to_orients{$transcript}->{'+'} || 0;
my $orient_minus = $transcript_to_orients{$transcript}->{'-'} || 0;
my $total_reads = $orient_plus + $orient_minus;
$transcript_to_orients{$transcript}->{'transcript'} = $transcript;
$transcript_to_orients{$transcript}->{'total_reads'} = $total_reads;
}
####
my @structs = values %transcript_to_orients;
@structs = reverse sort {$a->{total_reads}<=>$b->{total_reads}} @structs;
my $num_transcripts = scalar(@structs);
my $max_index = int($top_percent/100 * $num_transcripts);
# header
print join("\t", "#transcript", "minus_strand_1stReads", "plus_strand_1stReads", "total_reads", "pct_RF_SS") . "\n";
for (0..$max_index) {
my $struct = shift @structs;
my ($plus, $minus, $total_reads, $transcript) = ($struct->{'+'},
$struct->{'-'},
$struct->{'total_reads'},
$struct->{'transcript'});
unless ($plus) { $plus = 0; }
unless ($minus) { $minus = 0; }
# assuming RF
my $pct_total = $minus / $total_reads * 100;
print join("\t", $transcript, $minus, $plus, $total_reads, sprintf("%.1f", $pct_total)) . "\n";
}
exit(0);
}
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