rsem v1.1.9

[rsem.git] / rsem-calculate-expression

diff --git a/rsem-calculate-expression b/rsem-calculate-expression
index 0f22282dfc8f0b4ea259d057b7aca3ebdc2528ce..93fabce4686c8d0b7e4fafeae279c6262e7d412e 100755 (executable)
--- a/rsem-calculate-expression
+++ b/rsem-calculate-expression
@@ -15,7 +15,7 @@ my $NSPC = 50;
 
 my $NMB = 1024; # default
 
-my $status;
+my $status = 0;
 
 my $read_type = 1; # default, single end with qual
 
@@ -55,6 +55,9 @@ my $keep_intermediate_files = 0;
 
 my $strand_specific = 0;
 
+my $mTime = 0;
+my ($time_start, $time_end, $time_alignment, $time_rsem, $time_ci) = (0, 0, 0, 0, 0);
+
 GetOptions("keep-intermediate-files" => \$keep_intermediate_files,
           "no-qualities" => \$no_qual,
           "paired-end" => \$paired_end,
@@ -82,6 +85,7 @@ GetOptions("keep-intermediate-files" => \$keep_intermediate_files,
           "out-bam" => \$genBamF,
           "calc-ci" => \$calcCI,
           "ci-memory=i" => \$NMB,
+          "time" => \$mTime,
           "q|quiet" => \$quiet,
           "h|help" => \$help) or pod2usage(-exitval => 2, -verbose => 2);
 
@@ -113,7 +117,7 @@ my $mate1_list = "";
 my $mate2_list = "";
 my $inpF = "";
 
-my ($refName, $taskName, $tmp_dir, $imdName) = ();
+my ($refName, $sampleName, $sampleToken, $temp_dir, $stat_dir, $imdName) = ();
 my $gap = 32;
 
 if ($paired_end) {
@@ -129,30 +133,31 @@ if (scalar(@ARGV) == 3) {
     if ($is_sam || $is_bam) { $inpF = $ARGV[0]; } 
     else {$mate1_list = $ARGV[0]; }
     $refName = $ARGV[1];
-    $taskName = $ARGV[2];
+    $sampleName = $ARGV[2];
 }
 else {
     $mate1_list = $ARGV[0];
     $mate2_list = $ARGV[1];
     $refName = $ARGV[2];
-    $taskName = $ARGV[3];
+    $sampleName = $ARGV[3];
 }
 
-$tmp_dir = $taskName.".temp";
-my $pos = rindex($taskName, '/');
-if ($pos < 0) {
-    $imdName = "$tmp_dir/$taskName"; 
-}
-else {
-    $imdName = $tmp_dir."/".substr($taskName, $pos + 1);
-}
+my $pos = rindex($sampleName, '/');
+if ($pos < 0) { $sampleToken = $sampleName; }
+else { $sampleToken = substr($sampleName, $pos + 1); }
+
+$temp_dir = "$sampleName.temp";
+$stat_dir = "$sampleName.stat";
+
+if (!(-d $temp_dir) && !mkdir($temp_dir)) { print "Fail to create folder $temp_dir.\n"; exit(-1); }
+if (!(-d $stat_dir) && !mkdir($stat_dir)) { print "Fail to create folder $stat_dir.\n"; exit(-1); }
+
+$imdName = "$temp_dir/$sampleToken";
 
 if (!$is_sam && !$is_bam && $phred33 + $phred64 + $solexa == 0) { $phred33 = 1; }
 
 my ($mate_minL, $mate_maxL) = (1, $maxL);
 
-if (!(-d $tmp_dir) && !mkdir($tmp_dir)) { print "Fail to create the directory.\n"; exit(-1); }
-
 if ($bowtie_path ne "") { $bowtie_path .= "/"; }
 
 my ($fn, $dir, $suf) = fileparse($0);
@@ -173,7 +178,7 @@ if (!$is_sam && !$is_bam) {
     if ($read_type == 2 || $read_type == 3) { $command .= " -I $minL -X $maxL"; }
     
     if ($strand_specific || $probF == 1.0) { $command .= " --norc"; }
-    elsif ($probF = 0.0) { $command .= " --nofw"; }
+    elsif ($probF == 0.0) { $command .= " --nofw"; }
 
     $command .= " -p $nThreads -a -m $maxHits -S";
     if ($quiet) { $command .= " --quiet"; }
@@ -188,7 +193,13 @@ if (!$is_sam && !$is_bam) {
 
     $command .= " | gzip > $imdName.sam.gz";
     print "$command\n";
+
+    if ($mTime) { $time_start = time(); }
+
     $status = system($command);
+
+    if ($mTime) { $time_end = time(); $time_alignment = $time_end - $time_start; }
+
     if ($status != 0) {
        print "bowtie failed! Please check if you provide correct parameters/options for the pipeline!\n";
        exit(-1);
@@ -199,7 +210,9 @@ if (!$is_sam && !$is_bam) {
     $is_sam = 1; # output of bowtie is a sam file
 }
 
-$command = $dir."rsem-parse-alignments $refName $imdName";
+if ($mTime) { $time_start = time(); }
+
+$command = $dir."rsem-parse-alignments $refName $sampleName $sampleToken";
 
 my $samInpType;
 if ($is_sam) { $samInpType = "s"; } 
@@ -233,8 +246,8 @@ if ($status != 0) {
 }
 print "\n";
 
-$status = open(OUTPUT, ">$imdName.mparams");
-if ($status == 0) { print "Cannot generate $imdName.mparams!\n"; exit(-1); }
+my $doesOpen = open(OUTPUT, ">$imdName.mparams");
+if ($doesOpen == 0) { print "Cannot generate $imdName.mparams!\n"; exit(-1); }
 print OUTPUT "$minL $maxL\n";
 print OUTPUT "$probF\n";
 print OUTPUT "$estRSPD\n";
@@ -244,7 +257,7 @@ print OUTPUT "$mean $sd\n";
 print OUTPUT "$L\n";
 close(OUTPUT);  
 
-$command = $dir."rsem-run-em $refName $read_type $imdName $taskName -p $nThreads";
+$command = $dir."rsem-run-em $refName $read_type $sampleName $sampleToken -p $nThreads";
 if ($genBamF) { 
     $command .= " -b $samInpType $inpF";
     if ($fn_list ne "") { $command .= " 1 $fn_list"; }
@@ -262,7 +275,7 @@ if ($status != 0) {
 print "\n";
 
 if ($genBamF) {
-    $command = $dir."sam/samtools sort $taskName.bam $taskName.sorted";
+    $command = $dir."sam/samtools sort $sampleName.bam $sampleName.sorted";
     print "$command\n";
     $status = system($command);
     if ($status != 0) {
@@ -270,7 +283,7 @@ if ($genBamF) {
        exit(-1);
     }
     print "\n";
-    $command = $dir."sam/samtools index $taskName.sorted.bam";
+    $command = $dir."sam/samtools index $sampleName.sorted.bam";
     print "$command\n";
     $status = system($command);
     if ($status != 0) {
@@ -280,11 +293,16 @@ if ($genBamF) {
     print "\n";
 }
 
-&collectResults("$imdName.iso_res", "$taskName.isoforms.results"); # isoform level
-&collectResults("$imdName.gene_res", "$taskName.genes.results"); # gene level
+&collectResults("$imdName.iso_res", "$sampleName.isoforms.results"); # isoform level
+&collectResults("$imdName.gene_res", "$sampleName.genes.results"); # gene level
+
+if ($mTime) { $time_end = time(); $time_rsem = $time_end - $time_start; }
+
+if ($mTime) { $time_start = time(); }
 
 if ($calcCI) {
-    $command = $dir."rsem-run-gibbs $refName $taskName $imdName $BURNIN $CHAINLEN $SAMPLEGAP";
+    $command = $dir."rsem-run-gibbs $refName $sampleName $sampleToken $BURNIN $CHAINLEN $SAMPLEGAP";
+#    $command .= " -p $nThreads";
     if ($quiet) { $command .= " -q"; }
     print "$command\n";
     $status = system($command);
@@ -294,12 +312,12 @@ if ($calcCI) {
     }
     print "\n";
 
-    system("mv $taskName.isoforms.results $imdName.isoforms.results.bak1");
-    system("mv $taskName.genes.results $imdName.genes.results.bak1");
-    &collectResults("$imdName.iso_res", "$taskName.isoforms.results"); # isoform level
-    &collectResults("$imdName.gene_res", "$taskName.genes.results"); # gene level
+    system("mv $sampleName.isoforms.results $imdName.isoforms.results.bak1");
+    system("mv $sampleName.genes.results $imdName.genes.results.bak1");
+    &collectResults("$imdName.iso_res", "$sampleName.isoforms.results"); # isoform level
+    &collectResults("$imdName.gene_res", "$sampleName.genes.results"); # gene level
 
-    $command = $dir."rsem-calculate-credibility-intervals $refName $taskName $imdName $CONFIDENCE $NSPC $NMB";
+    $command = $dir."rsem-calculate-credibility-intervals $refName $sampleName $sampleToken $CONFIDENCE $NSPC $NMB";
     if ($quiet) { $command .= " -q"; }
     print "$command\n";
     $status = system($command);
@@ -309,20 +327,36 @@ if ($calcCI) {
     }
     print "\n";
 
-    system("mv $taskName.isoforms.results $imdName.isoforms.results.bak2");
-    system("mv $taskName.genes.results $imdName.genes.results.bak2");
-    &collectResults("$imdName.iso_res", "$taskName.isoforms.results"); # isoform level
-    &collectResults("$imdName.gene_res", "$taskName.genes.results"); # gene level
+    system("mv $sampleName.isoforms.results $imdName.isoforms.results.bak2");
+    system("mv $sampleName.genes.results $imdName.genes.results.bak2");
+    &collectResults("$imdName.iso_res", "$sampleName.isoforms.results"); # isoform level
+    &collectResults("$imdName.gene_res", "$sampleName.genes.results"); # gene level
 }
 
+if ($mTime) { $time_end = time(); $time_ci = $time_end - $time_start; }
+
+if ($mTime) { $time_start = time(); }
+
 if (!$keep_intermediate_files) {
-    $status = system ("rm -rf $tmp_dir");
+    $status = system("rm -rf $temp_dir");
     if ($status != 0) {
        print "Fail to delete the temporary folder!\n";
        exit(-1);
     }
 }
 
+if ($mTime) { $time_end = time(); }
+
+if ($mTime) { 
+    open(OUTPUT, ">$sampleName.time");
+    print OUTPUT "Alignment: $time_alignment s.\n";
+    print OUTPUT "RSEM: $time_rsem s.\n";
+    print OUTPUT "CI: $time_ci s.\n";
+    my $time_del = $time_end - $time_start;
+    print OUTPUT "Delete: $time_del s.\n";
+    close(OUTPUT);
+}
+
 # inpF, outF
 sub collectResults {
     my $local_status;
@@ -582,11 +616,6 @@ file. If no other attributes are given or no GTF file is provided in
 'rsem-prepare-reference', there will be no tab after the
 tau_value field.
 
-=item B<sample_name.model> and B<sample_name.theta>
-
-Output files used by RSEM internally for tasks like simulation,
-compute credibility intervals etc.
-
 =item B<sample_name.bam, sample_name.sorted.bam and sample_name.sorted.bam.bai>
 
 Only generated when --out-bam is specified.
@@ -604,6 +633,9 @@ representing the posterior probability.
 'sample_name.sorted.bam' and 'sample_name.sorted.bam.bai' are the
 sorted BAM file and indices generated by samtools (included in RSEM package).
 
+=item B<sample_name.stat>
+
+This is a folder instead of a file. All model related statistics are stored in this folder. Use 'rsem-plot-model' can generate plots using this folder.
 
 =back
 
@@ -661,3 +693,5 @@ Assume the path to the bowtie executables is in the user's PATH environment vari
                            mmliver_paired_end_quals
 
 =cut
+
+#  LocalWords:  usr