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|
#!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long qw(:config no_ignore_case bundling);
use Cwd;
$ENV{LC_ALL} = 'C';
my $util_dir = "/usr/lib/trinityrnaseq/util/support_scripts";
my $usage = <<_EOUSAGE_;
#########################################################################################
#
# Required:
#
# --iworm <string> inchworm assembled contigs
#
# --left <string> left fragment file
# --right <string> right fragment file
#
# or --single_but_really_paired <string> single read file containing both pairs.
#
# --seqType <string> fq|fa
#
# Optional (if strand-specific RNA-Seq):
#
# --work_dir <string> directory to perform data processing (default: workdir.\$pid
#
# --SS_lib_type <string> RF or FR
#
# --CPU <int> default: 2
#
###########################################################################################
_EOUSAGE_
;
my $inchworm_contigs;
my $left_file;
my $right_file;
my $single_file;
my $seqType;
my $SS_lib_type;
my $work_dir;
my $CPU = 2;
&GetOptions( 'iworm=s' => \$inchworm_contigs,
'left=s' => \$left_file,
'right=s' => \$right_file,
'seqType=s' => \$seqType,
'SS_lib_type=s' => \$SS_lib_type,
'work_dir=s' => \$work_dir,
'CPU=i' => \$CPU,
'single_but_really_paired=s' => \$single_file,
);
unless ($inchworm_contigs && ($single_file || ($left_file && $right_file)) && $seqType) {
die $usage;
}
unless ($work_dir) {
$work_dir = cwd() . "/jaccard_clip_workdir";
unless (-d $work_dir) {
mkdir($work_dir) or die "Error, cannot mkdir $work_dir";
}
}
main: {
my $curr_dir = cwd();
# create full paths to inputs, if not set.
foreach my $file ($inchworm_contigs, $left_file, $right_file, $single_file) {
unless ($file) { next; }
unless ($file =~ /^\//) {
$file = "$curr_dir/$file";
}
}
my $outdir = $work_dir;
unless (-d $outdir) {
mkdir ($outdir) or die "Error, cannot mkdir $outdir";
}
my $target_iworm_fa = "$outdir/iworm.fa";
&process_cmd("ln -s $inchworm_contigs $target_iworm_fa") unless (-e $target_iworm_fa);
## run the bowtie alignment pipeline
my $bowtie_out = "$outdir";
my $cmd = "";
if ($left_file && $right_file) {
$cmd = "$util_dir/bowtie2_wrapper.pl --seqType $seqType --left $left_file --right $right_file --CPU $CPU --target $target_iworm_fa -o $bowtie_out/bowtie2";
}
else {
$cmd = "$util_dir/bowtie2_wrapper.pl --seqType $seqType --single $single_file --CPU $CPU --target $target_iworm_fa -o $bowtie_out/bowtie2";
}
if ($SS_lib_type) {
$cmd .= " --SS_lib_type $SS_lib_type ";
}
chdir $outdir or die "Error, cannot cd to $outdir";
&process_cmd($cmd);
my $final_bam_file = ($SS_lib_type) ? "$bowtie_out/bowtie2.coordSorted.bam.+.bam" : "$bowtie_out/bowtie2.coordSorted.bam";
my $alignment_file = "bowtie_alignments.for_jaccard.bam";
&process_cmd("ln -sf $final_bam_file $alignment_file");
## run Jaccard computation:
my $jaccard_wig_file = "$alignment_file.J100.wig";
my $frag_coords_file = "$alignment_file.frag_coords";
&process_cmd("$util_dir/SAM_ordered_pair_jaccard.pl --sam $alignment_file -W 100 > $jaccard_wig_file") unless (-s $jaccard_wig_file && -s $frag_coords_file);
# The above creates a .frag_coords file. Use this to compute fragment-level coverage
my $frag_coverage_file = "$frag_coords_file.wig";
&process_cmd("$util_dir/fragment_coverage_writer.pl $frag_coords_file > $frag_coverage_file") unless (-e $frag_coverage_file);
## define the transcript clip points:
my $clips_file = "$jaccard_wig_file.clips";
&process_cmd("$util_dir/jaccard_wig_clipper.pl --jaccard_wig $jaccard_wig_file --coverage_wig $frag_coverage_file > $clips_file") unless (-e $clips_file) ;
## clip the inchworm transcripts:
&process_cmd("$util_dir/jaccard_fasta_clipper.pl $inchworm_contigs $clips_file > $inchworm_contigs.clipped.fa") unless (-e "$inchworm_contigs.clipped.fa");
exit(0);
}
####
sub process_cmd {
my ($cmd) = @_;
print "CMD: $cmd\n";
my $ret = system($cmd);
if ($ret) {
die "Error, cmd: $cmd died with ret $ret";
}
return($ret);
}
|
