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|
#!/usr/bin/env perl
use strict;
use warnings;
use lib ("$ENV{TRINITY_HOME}/PerlLib/");
use Fasta_reader;
use Cwd;
use Data::Dumper;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use List::Util qw (shuffle);
my $help_flag;
my $usage = <<__EOUSAGE__;
################################################################################
$0
################################################################################
#
# * Required:
#
# --ref_trans|R <string> reference transcriptome
#
# --out_dir|O <string> output directory name
#
# --read_length <int> default: 76
#
# --frag_length <int> default: 300
#
# --depth_of_cov <int> default: 100
#
#
####
#
# 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 $OUT_DIR;
my $ref_trans_fa;
my $read_length = 76;
my $frag_length = 300;
my $depth_of_cov = 100;
&GetOptions ( 'help' => \$help_flag,
# required
'ref_trans|R=s' => \$ref_trans_fa,
# optional
'out_dir|O=s' => \$OUT_DIR,
'read_length=i' => \$read_length,
'frag_length=i' => \$frag_length,
'depth_of_cov=i' => \$depth_of_cov,
);
if ($help_flag) {
die $usage;
}
unless ($ref_trans_fa && $OUT_DIR) {
die $usage;
}
unless ($ENV{TRINITY_HOME}) {
$ENV{TRINITY_HOME} = "/usr/lib/trinityrnaseq";
}
main: {
my $BASEDIR = cwd();
unless ($ref_trans_fa =~ /^\//) {
$ref_trans_fa = "$BASEDIR/$ref_trans_fa";
}
unless (-d $OUT_DIR) {
&process_cmd("mkdir -p $OUT_DIR");
}
chdir $OUT_DIR or die "Error, cannot cd to $OUT_DIR";
my $cmd = "";
# simulate reads:
$cmd = "$ENV{TRINITY_HOME}/util/misc/simulate_illuminaPE_from_transcripts.wgsim.pl --transcripts $ref_trans_fa "
. " --read_length $read_length "
. " --frag_length $frag_length "
. " --depth_of_cov 200 "
. " @ARGV "; # wgsim opts pass-through
;
## todo: add mutation rate info
&process_cmd($cmd);
}
####
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;
}
|
