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|
#!/usr/bin/env perl
use strict;
use warnings;
use threads;
use Getopt::Long qw(:config no_ignore_case bundling);
use lib ("/usr/lib/trinityrnaseq/PerlLib");
use WigParser;
use Fasta_reader;
use Statistics::Descriptive;
my $usage = <<_EOUSAGE_;
########################################################################################################
#
# Required:
#
# --coord_sorted_SAM <string> coordinate-sorted SAM file.
# --transcripts <string> transcripts in fasta file format
#
# *If Strand-specific, specify:
# --SS_lib_type <string> library type: if single: F or R, if paired: FR or RF
# --trim_pct_median <int> percent of median coverage value to set as upper threshold for end-trimming (default: 10)
#
# --no_trim just provide the coverage info
#
########################################################################################################
_EOUSAGE_
;
my $help_flag;
#my $partition_join_size;
my $SAM_file;
my $SS_lib_type = "";
my $transcripts_fasta_file = "";
my $trim_pct_median = 10;
my $NO_TRIM = 0;
&GetOptions ( 'h' => \$help_flag,
'coord_sorted_SAM=s' => \$SAM_file,
'SS_lib_type=s' => \$SS_lib_type,
'transcripts=s' => \$transcripts_fasta_file,
'trim_pct_median=i' => \$trim_pct_median,
'no_trim' => \$NO_TRIM,
);
if ($help_flag) {
die $usage;
}
unless (
$SAM_file
&&
$transcripts_fasta_file
) {
die $usage;
}
if ($SS_lib_type && $SS_lib_type !~ /^(F|R|FR|RF)$/) {
die "Error, invalid --SS_lib_type, only F, R, FR, or RF are possible values";
}
my $UTIL_DIR = "/usr/lib/trinityrnaseq/util/support_scripts";
main: {
my $sam_file_to_process;
if ($SS_lib_type) {
$sam_file_to_process = "$SAM_file.+.sam";
my $cmd = "$UTIL_DIR/SAM_strand_separator.pl $SAM_file $SS_lib_type";
&process_cmd($cmd) unless (-s $sam_file_to_process);
}
else {
$sam_file_to_process = $SAM_file;
}
## define fragments
my $cmd = "$UTIL_DIR/SAM_to_frag_coords.pl --sam $sam_file_to_process --min_insert_size 1 --max_insert_size 1000 "; ## writes file: $sam_file.frag_coords
&process_cmd($cmd) unless (-s "$sam_file_to_process.frag_coords");
## define coverage
$cmd = "$UTIL_DIR/fragment_coverage_writer.pl $sam_file_to_process.frag_coords > $sam_file_to_process.frag_coverage.wig";
&process_cmd($cmd) unless (-s "$sam_file_to_process.frag_coverage.wig");
my $wig_parser = new WigParser("$sam_file_to_process.frag_coverage.wig");
my $fasta_reader = new Fasta_reader($transcripts_fasta_file);
while (my $seq_obj = $fasta_reader->next()) {
my $acc = $seq_obj->get_accession();
my $sequence = $seq_obj->get_sequence();
my $trim_5p_pos = "NA";
my $trim_3p_pos = "NA";
my $median = 0;
my @cov = ();
eval {
# throws exception if there's no read coverage
@cov = $wig_parser->get_wig_array($acc);
#print ">$acc\n$sequence\n" . join(" ", @cov) . "\n";
my $stat = Statistics::Descriptive::Full->new();
$stat->add_data(@cov);
$median = $stat->median();
#print "Median: $median\n";
my $trim_thresh = int($trim_pct_median/100 * $median + 0.5);
if ($trim_thresh == 0) {
$trim_thresh = 1;
}
#print "Trim_thresh: $trim_thresh\n";
unless ($NO_TRIM) {
$trim_5p_pos = &trim_5p(\@cov, $trim_thresh);
$trim_3p_pos = &trim_3p(\@cov, $trim_thresh);
}
};
print join("\t", $acc, "$trim_5p_pos-$trim_3p_pos", $median, $sequence, join(" ", @cov) ) . "\n";
}
exit(0);
}
####
sub process_cmd {
my ($cmd) = @_;
print STDERR "CMD: $cmd\n";
my $ret = system($cmd);
if ($ret) {
die "Error, command $cmd died with ret $ret";
}
return;
}
####
sub trim_5p {
my ($cov_aref, $threshold) = @_;
for (my $i = 0; $i <= $#$cov_aref; $i++) {
my $cov = $cov_aref->[$i];
if ($cov >= $threshold) {
return($i+1);
}
}
return(-1); # bad sequence
}
####
sub trim_3p {
my ($cov_aref, $threshold) = @_;
for (my $i = $#$cov_aref; $i >=0; $i--) {
my $cov = $cov_aref->[$i];
if ($cov >= $threshold) {
return($i+1);
}
}
return(-1); # bad sequence
}
|
