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|
#!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use lib ("/usr/lib/trinityrnaseq/PerlLib");
use Fasta_reader;
use Nuc_translator;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use Cwd;
my $usage = <<__EOUSAGE__;
##################################################################
$0
##################################################################
#
# Required:
#
# --transcripts <string> file containing target transcripts in fasta format
#
# Optional:
#
# --read_length <int> default: 76
#
# --frag_length <int> default: 300
#
# --out_prefix <string> default: 'reads'
#
# --depth_of_cov <int> default: 100 (100x targeted base coverage)
#
####
#
# following wgsim options are pass-through:
#
# Options:
# -e FLOAT base error rate [0.020]
# -s INT standard deviation [50]
# -r FLOAT rate of mutations [0.0010]
# -R FLOAT fraction of indels [0.15]
# -X FLOAT probability an indel is extended [0.30]
# -S INT seed for random generator [-1]
# -A FLOAT disgard if the fraction of ambiguous bases higher than FLOAT [0.05]
# -h haplotype mode
# -Z INT strand specific mode: 1=FR, 2=RF
# -D debug mode... highly verbose
#
#
############################################################################################
__EOUSAGE__
;
my $require_proper_pairs_flag = 0;
my $transcripts;
my $read_length = 76;
my $frag_length = 300;
my $help_flag;
my $out_prefix = "reads";
my $depth_of_cov = 100;
&GetOptions ( 'help' => \$help_flag,
'transcripts=s' => \$transcripts,
'read_length=i' => \$read_length,
'frag_length=i' => \$frag_length,
'out_prefix=s' => \$out_prefix,
'depth_of_cov=i' => \$depth_of_cov,
);
if ($help_flag) {
die $usage;
}
unless ($transcripts) {
die $usage;
}
unless ($out_prefix =~ /^\//) {
$out_prefix = cwd() . "/$out_prefix";
}
main: {
my $number_reads = &estimate_total_read_count($transcripts, $depth_of_cov, $read_length);
my $cmd = "wgsim-trans -N $number_reads -1 $read_length -2 $read_length "
. " -d $frag_length "
. " @ARGV > $out_prefix.log"; # pass-through to wgsim
my $token = "wgsim_R${read_length}_F${frag_length}_D${depth_of_cov}";
if (grep { "-Z" } @ARGV) {
$token .= "_SS";
}
my $left_prefix = "$out_prefix.$token.left";
my $right_prefix = "$out_prefix.$token.right";
$cmd .= " $transcripts $left_prefix.fq $right_prefix.fq";
&process_cmd($cmd);
# convert to fasta format
&process_cmd("/usr/lib/trinityrnaseq/util/support_scripts/fastQ_to_fastA.pl -I $left_prefix.fq > $left_prefix.fa");
&process_cmd("/usr/lib/trinityrnaseq/util/support_scripts/fastQ_to_fastA.pl -I $right_prefix.fq > $right_prefix.fa");
#unlink("$left_prefix.fq", "$right_prefix.fq");
open(my $ofh, ">$out_prefix.$token.info") or die "Error, cannot write to file: $out_prefix.$token.info";
print $ofh join("\t", $transcripts, "$left_prefix.fa", "$right_prefix.fa");
close $ofh;
exit(0);
}
####
sub estimate_total_read_count {
my ($transcripts_fasta_file, $depth_of_cov, $read_length) = @_;
my $sum_seq_length = 0;
my $fasta_reader = new Fasta_reader($transcripts);
while (my $seq_obj = $fasta_reader->next()) {
my $sequence = $seq_obj->get_sequence();
$sum_seq_length += length($sequence);
}
# DOC = num_reads * read_length * 2 / seq_length
# so,
# num_reads = DOC * seq_length / 2 / read_length
my $num_reads = $depth_of_cov * $sum_seq_length / 2 / $read_length;
$num_reads = int($num_reads + 0.5);
return($num_reads);
}
####
sub process_cmd {
my ($cmd) = @_;
print STDERR "CMD: $cmd\n";
my $ret = system($cmd);
if ($ret) {
die "Error, cmd: $cmd died with ret $ret";
}
return;
}
|
