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|
#!/usr/bin/env perl
use strict;
use warnings;
use lib ("/usr/lib/trinityrnaseq/PerlLib");
use Gene_obj;
use GFF3_utils;
use SAM_reader;
use SAM_entry;
use Fasta_reader;
use Data::Dumper;
use Getopt::Long qw(:config no_ignore_case bundling);
my $usage = <<_EOUSAGE_;
###################################################################
#
# --encoded_fa <string> feature-encoded fasta file
#
# --coord_sorted_sam <string> sam alignment file
#
# Optional:
#
# --SS_lib_type <string> [FR,RF] (paired), or [R,F] (single)
#
##################################################################
_EOUSAGE_
;
my $encoded_fa;
my $sam_file;
my $SS_lib_type;
my $help;
&GetOptions ( 'h' => \$help,
'encoded_fa=s' => \$encoded_fa,
'coord_sorted_sam=s' => \$sam_file,
'SS_lib_type=s' => \$SS_lib_type,
);
if ($help) {
die $usage;
}
if (! ($encoded_fa && $sam_file) ) {
die $usage;
}
my %SS_encoding = ( 0 => 'intergenic',
1 => 'intron',
2 => 'exon+',
3 => 'exon-',
4 => 'rRNA+',
5 => 'rRNA-',
);
my %reg_encoding = ( 0 => 'intergenic',
1 => 'intron',
2 => 'exon',
3 => 'exon',
4 => 'rRNA',
5 => 'rRNA',
);
main: {
print STDERR "-parsing genome encoding\n";
my $fasta_reader = new Fasta_reader($encoded_fa);
my %genome_encoding = $fasta_reader->retrieve_all_seqs_hash();
my %feature_coverage_counter;
print STDERR "-parsing sam file\n";
my $curr_scaffold = "";
my $feat_encoding = "";
#my @feats;
my $sam_reader = new SAM_reader($sam_file);
my $read_counter = 0;
while (my $sam_entry = $sam_reader->get_next()) {
$read_counter++;
print STDERR "\r[$read_counter] reads processed. " if ($read_counter % 1000 == 0);
if ($sam_entry->is_query_unmapped()) {
next;
}
my $scaffold = $sam_entry->get_scaffold_name();
if ($scaffold ne $curr_scaffold) {
$curr_scaffold = $scaffold;
$feat_encoding = $genome_encoding{$curr_scaffold} || ""; # no features on a contig are considered intergenic
#@feats = split(//, $feat_encoding);
#print "encoding: $feat_encoding, length: " . length($feat_encoding) . "\n";
}
my ($genome_coords_aref, $query_coords_aref) = $sam_entry->get_alignment_coords();
my $strand = ($SS_lib_type) ? $sam_entry->get_query_transcribed_strand($SS_lib_type) : $sam_entry->get_query_strand();
my $genome_coordset = shift @$genome_coords_aref;
my ($lend, $rend) = @$genome_coordset;
my $midpt = int( ($rend+$lend)/2);
my $encoding = 0;
if ($midpt -1 < length($feat_encoding)) {
$encoding = substr($feat_encoding, $midpt-1, 1);
}
my $feature_type = ($SS_lib_type) ? $SS_encoding{$encoding} : $reg_encoding{$encoding};
if ($SS_lib_type) {
if ($feature_type =~ /([\+\-])$/) {
my $feature_orient = $1;
if ($feature_orient eq $strand && $strand eq '-') {
# -,-
# consider it a forward feature
$feature_type =~ s/\-$/\+/;
}
elsif ($feature_orient ne $strand && $feature_orient eq '+') {
# Feature+,read- : make feature -
$feature_type =~ s/\+$/-/;
}
# Feature-, read+ : counting feature as anti, so already OK
# Feature+, read+ : counting feature as plus, so already OK
}
$feature_coverage_counter{$feature_type}++;
}
else {
## not strand-specific
$feature_coverage_counter{$feature_type}++;
}
}
my $total_coverage = 0;
foreach my $count (values %feature_coverage_counter) {
$total_coverage += $count;
}
print "\n\n";
foreach my $feature_type (sort keys %feature_coverage_counter) {
my $coverage = $feature_coverage_counter{$feature_type};
my $percent = sprintf("%.2f", $coverage/$total_coverage*100);
print join("\t", $feature_type, $coverage, "$percent\%") . "\n";
}
print "\n\n";
exit(0);
}
|
