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|
#!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use File::Basename;
use FindBin;
use Cwd;
my $usage = <<__EOUSAGE__;
###############################################################################
#
# Required:
#
# --target <string> : genome multifasta file
# --seqType <string> :type of reads ('fq' or 'fa')
#
# If paired reads:
# --left <string> :left reads
# --right <string> :right reads
#
# Or, if unpaired reads:
# --single <string> :single reads
#
# --output|-o <string> :name of directory for output
#
# -i <int> :min intron length
# -I <int> :max intron length
#
#
# Optional:
#
# --SS_lib_type <string> :strand-specific library type : {RF, FR, R, F} (RF =~ fr-firststrand)
# --CPU <int> :number of CPUs to use
#
# --GTF <string> :annotations to assist, provided in GTF file format
#
###############################################################################
__EOUSAGE__
;
my $help_flag;
my ($seqType, $left_file, $right_file, $single_file, $SS_lib_type, $output_dir, $CPU, $target_genome, $min_intron_length, $max_intron_length);
my $GTF_annots;
&GetOptions ( 'h' => \$help_flag,
## general opts
"seqType=s" => \$seqType,
"left=s" => \$left_file,
"right=s" => \$right_file,
"single=s" => \$single_file,
"target=s" => \$target_genome,
"SS_lib_type=s" => \$SS_lib_type,
"output|o=s" => \$output_dir,
'CPU=i' => \$CPU,
'GTF=s' => \$GTF_annots,
'i=i' => \$min_intron_length,
'I=i' => \$max_intron_length,
);
if (@ARGV) {
die "Error, do not understand options: @ARGV\n";
}
unless ($seqType && $target_genome && ( ($single_file) || ($left_file && $right_file) ) && $output_dir) {
die $usage;
}
if ($GTF_annots) {
## add full path
if ($GTF_annots !~ /^\//) {
$GTF_annots = cwd() . "/$GTF_annots";
}
}
main: {
my $util_dir = "$FindBin::RealBin/..";
#############################
## align reads using Tophat
#############################
my $cmd = "$util_dir/alignReads.pl --seqType $seqType --output $output_dir --aligner tophat2 --target $target_genome ";
if ($single_file) {
$cmd .= " --single $single_file ";
}
else {
$cmd .= " --left $left_file --right $right_file ";
}
if ($SS_lib_type) {
$cmd .= " --SS_lib_type $SS_lib_type ";
}
if ($min_intron_length) {
$cmd .= " -i $min_intron_length ";
}
if ($max_intron_length) {
$cmd .= " -I $max_intron_length ";
}
if ($CPU || $GTF_annots) {
$cmd .= " -- ";
if ($CPU) {
$cmd .= " -p $CPU ";
}
if ($GTF_annots) {
$cmd .= " --GTF $GTF_annots ";
my $transcriptome_index_dir = "$GTF_annots.tuxedo_indices";
if (-d $transcriptome_index_dir) {
my $prefix = basename($GTF_annots);
$prefix =~ s/\.[^\.]+$//;
$cmd .= " --transcriptome-index $transcriptome_index_dir/$prefix ";
}
else {
#die "Error, cannot find: $transcriptome_index_dir";
print STDERR "WARNING: cannot find pre-built index for $GTF_annots; this will slow it down.\n";
}
}
}
&process_cmd($cmd);
#######################################
# assemble transcripts using cufflinks
#######################################
my $tophat_alignment_bam = "$output_dir/tophat_out/accepted_hits.bam";
$cmd = "cufflinks --no-update-check --upper-quartile-norm -o $output_dir/cuff_out ";
if ($GTF_annots) {
$cmd .= " --GTF-guide $GTF_annots ";
}
if ($SS_lib_type) {
my %tuxedo_lib_type = (RF => "fr-firststrand",
R => "fr-firststrand",
FR => "fr-secondstrand",
F => "fr-secondstrand",
);
my $lib_type = $tuxedo_lib_type{$SS_lib_type} or die "Error, cannot determine tophat lib_type based on SS_lib_type: $SS_lib_type ";
$cmd .= " --library-type $lib_type ";
}
if ($CPU) {
$cmd .= " -p $CPU ";
}
$cmd .= " $tophat_alignment_bam ";
&process_cmd($cmd);
exit(0);
}
####
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;
}
|
